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440 V. C. Santos et al.
hydroxylamine pentanamide inhibitor (compound 1; Fig. 15.2d). This analysis revealed that the carbonyl moieties maintained alignment with the water molecule, even with the incorporation of an amine into the backbonedenoted by the substi­tution of Phe and tert-but yl carbamate moieties with the decahydroisoquinoline tert­butylamide.
Studies with compound 1 showed a better pharmacokinetic prole than the hydroxyethylene isostere inhibitor. However, compound 1 exhibited moderate potency against viral dissemination in infected human T cells with cell culture inhibitory concentration (CIC
) values of 400 nM. Thus, considering the informa-
95
tion obtained from molecular modeling studies, structural modications were explored, leading to the development of indinavir (Fig. 15.2e ), which exhibited a CIC
of 50 nM and an oral bioavailability of approximately 63% [26]. Indinavir,
95
under the brand Crixivan
®
, was approved in 1996 as a treatment for HIV/AIDS [32].
Finally, it is important to emphasize that other rst-generation HIV-1 protease inhibitors were developed and approved, such as ritonavir, nelnavir, and amprenavir. However, the emergence of HIV-resistant strains led to the development of the so-called second-generation inhibitors.
2.3 Drug Resistance and Second-Generation HIV Protease
Inhibitors
The development of ritonavir, a rst-generation inhibitor, provided relevant infor­mation for developing lopinavir. Ritonavir is a potent inhibitor (K
of 0.015 nM),
i
which was approved by the FDA in 1996 (Fig. 15.3a). Studies conducted with ritonavir-treated patients revealed substitutions at nine different codons in the protease gene, with mutants at Val82* being the rst to emerge in infected patients [33]. This information motivated the search for inhibitors that would not interact with Val82*, making mutations at this position less likely to induce drug resistance.
The synthesis of DNA from a viral RNA is catalyzed by the viral reverse transcriptase. This process has a high error propensity, mainly attributable to the enzymes elevated mismatch error rate (10
-3
–10-5nucleotide bases per cycle) and its absence of proofreading activity. Thus, this phenomenon allows the emergence of polymorphic mutations within HIV-1 genome [34]. Several factors, such as delete­rious mutations, natural selection, and the host immune response, constrict the proliferation of mutated strains within a specied timeframe [35]. The introduction of antiretroviral treatment exerts novel selection pressures that may contribute to the proliferation of drug-resistant strains.
Primary mutations frequently occur in residues near the active site involved in substrate binding. These mutations affect electrostatic and van der Waals interac­tions between the enzyme and the inhibitor, frequently reducing binding afnity
15 Molecular Modeling Strategies in Drug Design, Development, and... 441
[36]. Importantly, these modications can also undermine the prociency of sub­strate processing, adversely impacting virus replication [37]. Conversely, secondary mutations are located outside the active site and may compensate for the deleterious effects of primary mutations on substrate processing while maintaining drug resis­tance [38, 39].
Many specic primary and secondary mutations in HIV protease are associated with different inhibitors, and strategies have been developed to design inhibitors that interact with the HIV protease in a way that creates a higher barrier to resistance. Here we discuss the development process of two second-generation inhibitors, lopinavir, and darunavir.
2.3.1 Lopinavir
Structural analysis, based on the X-ray crystal structure of wild-type HIV-1 protease, revealed an interaction between ritonavirs P3 isopropylthiazolyl group and the
Fig. 15.3 Structure-based development of lopinavir. Chemical structure of ritonavir (a) and its binding mode (PDB ID: 1HXW) in the HIV-1 protease active site (b). Chemical structures of the cyclic urea compound, A-155564 (c), lopinavir (d), and the binding mode of lopinavir (PDB ID: 1MUI) in the HIV-1 protease active site (e). The isopropylthiazolyl group of ritonavir and the Val82* residues are highlighted by black dashed lines. The same region is highlighted for the HIV-1 protease structure bound to lopinavir. Residues in chain B are identied by the letter and number followed by *. Hydrogen bonds are shown as yellow dashed lines. Important residues and compounds are represented as sticks and colored by atom. Carbons are colored gray in the enzyme and green or cyan in the compounds. (Figure produced using ChemDraw and PyMOL)
442 V. C. Santos et al.
Val82* residue (Fig. 15.3b)[40]. To develop an inhibitor with activity less depen- dent on an interaction with Val82*, researchers removed the P3 isopropylthiazolyl group from ritonavir. However, this reduction decreased the protease afnity, resulting in a 30-fold lower anti-HIV activity (EC (EC
= 0.06 μM). A conformation constraint introduced by a cyclic urea compound
50
= 1.8 μM) compared to ritonavir
50
(compound A-155564; Fig. 15.3c) resulted in improved anti-HIV activity (EC
= 0.15 μM), and the substitution of the P2group with a dimethyl phenoxy
50
acetyl group in lopinavir (Fig. 15.3d), which exhibited an EC50of 0.01 μM and a K of 1.3 pM for the wild-type protease compared to ritonavir s Kiof 10 pM. Moreover, lopinavir demonstrated higher potency than ritonavir against proteases with muta­tions in Val82*, such as a K
of 3.7 pM for the V82F mutant HIV protease compared
i
to ritonavirs Ki of 520 pM [10].
To comprehend the enhanced binding afnity of lopinavir towards both wild-type and mutant proteases, researchers modeled the inhibitor within the active site of the protease based on a crystal structure of the complex with ritonavir. In this model, the 2,6-dimethylphenoxy group was positioned in the S2subsite to ll the available space, while the valinyl-cyclic urea moiety was rotated within the S2 subsite to ensure optimal hydrogen bonding with Asp29 or Asp30 [10, 41]. As expected, the model suggested that the P3 region of lopinavir engaged in minimal interactions with Val82*, as later conrmed by X-ray crystallography (Fig. 15.3e)[41].
Ritonavir, originally approved in 1996, was later found to be a potent inhibitor of cytochrome P450 3A, a key metabolic enzyme for protease inhibitors. Taking advantage of this property, lopinavir and ritonavir were combined into a single pill marketed as Kaletra
®
, approved in 2000 for the treatment of HIV infections [42].
i
2.3.2 Darunavir
Moreover, considering the approaches to avoid or overcome resistance, the back­bone bindingstrategy has also been adopted. In this approach, the goal is to design inhibitors that maximize inhibitor-backbone hydrogen-bonding interactions. This concept arose from a structural analysis comparing X-ray structures of diverse mutant HIV proteases with those of the wild-type HIV protease, revealing only minimal distortions on the backbone conformation within the active site [43, 44]. The backbone binding strategy guided the structure-based design of darunavira non-peptidic inhibitor. To improve water solubility and bioavailability, research focused on designing non-peptidic cyclic or heterocyclic structures, partic­ularly cyclic ether or polyether-derived ligands.
Initially, researchers developed a cyclic ether-derived ligand (compound 2, Fig. 15.4a) based on the X-ray structure of saquinavir , which exhibited an IC
of
50
132 nM against the enzyme. Subsequently, an X-ray crystal structure of this ligand revealed a potential weak interaction between the oxygen atom of the tetrahydrofu­ran ring and the backbone nitrogen atoms of residues Asp29 and Asp30 [45]. To strengthen the interacti on with these residues, researchers synthesized compounds featuring bicyclic tetrahydrofuran rings (bis-THF), resulting in a higher potency
15 Molecular Modeling Strategies in Drug Design, Development, and... 443
Fig. 15.4 The development of darunavir. Chemical structures of a cyclic ether-derived ligand, compound 2 (a), TMC-126 (b), and darunavir (c). Binding mode of darunavir (PDB ID: 2IEO) to the HIV-1 protease mutant I84V active site (d). Water molecules are represented as red spheres, and the hydrogen bonds are shown as yellow dashed lines. Residues in chain B are identied by the letter and number followed by *. Important residues and compounds are represented as sticks and colored by atom. Carbons are colored gray in the enzyme and green in the compound. (Figure produced using ChemDraw and PyMOL)
against the enzyme (IC50= 1.8 nM) and enhanced water solubility [46]. The impact of bis-THF on potency enhancement was further investigated in the context of other isosteres [47], culminating in the development of TMC-126, with a K
of 14 pM
i
(Fig. 15.4b). To better understand the potential interactions with this inhibitor, researchers conducted structural modeling of the HIV-1 protease complexed with TMC-126. They utilized published crystal structures of HIV-1 protease complexed with amprenavir, as well as with various inhibitors containing bis-THF, followed by minimization of the active site using the Sybyl force eld [48]. Consistent with previous studies demonstrating higher potency with the substitution of THF by a bis-THF group, the model suggests this heightened potency to be linked to hydrogen bonding interactions between the oxygen atoms of the bis-THF moiety and the main­chain amides of Asp29* and Asp30* residues.
Subsequently, incorporating bis-THF into a p-amino sulfonamide isostere led to the development of darunavir (Fig. 15.4c). X-ray crystallography studies involving darunavir complexed with mutant proteases revealed that the interactions between the bis- THF group and the amides of Asp29* and Asp30* remained intact, while
444 V. C. Santos et al.
new polar interactions were also observed with the side-chain carboxylate of Asp30 (Fig. 15.4d)[49].
In addition to the backbone strategy, another approach to avoid drug resistance is based on the substrate-envelope hypothesis. Viral polyproteins, subject to processing by HIV protease, undergo adaptive changes that culminate in forming a conserved substrate envelope upon binding with the enzymes active site [39]. The substrate­envelope hypothesis suggests that the overall substrate conformation is pivotal in achieving effective binding, not just the amino acid sequence. Mutations near this substrate envelope signicantly diminish the proteasesaffinity for its substrates, rendering them unfavorable. Consequently, developing protease inhibitors strategi­cally aligned with the substrate envelope should prevent the emergence of drug­resistance mutations.
Although the development of darunavir was not based on the substrate-envelope hypothesis, subsequent studies have shown that it ts the consensus substrate volume [50]. As expected for a drug complying both with the backbone-binding strategy and the substrate-envelope hypothesis, darunavir is a non-peptidic inhibitor of HIV-1 protease with high potency against drug-resistant HIV variants [11, 51]. Darunavir, sold under the brand name Prezista 2006, and it is part of antiretroviral therapy for people infected with HIV. Another virus disease for which antiviral drugs were developed with the aid of molecular modeling techniques is hepatitis C and it will be discussed in the following section.
®
, was rst approved in
3 Structure-Based Drug Design of Grazoprevir
and Voxilaprevir as Hepatitis C Virus (HCV) NS3/4a Protease Inhibitors
In 1989, scientists isolated the so-called non-A and non-B hepatitis agents [52]. HCV infection occurs mainly in the liver and has an incubation period of 2–12 weeks, which is followed by an acute asymptomatic phase that is often undiagnosed. When symptoms appear, they can be fever, tiredness, loss of appetite, nausea and vomiting, abdominal pain, dark urine, pale feces, joint pain, and jaundice [53]. The infection follows two courses: spontaneous clearance (18–34%) of infected individuals or progression to chronic infection [54]. HCV can be found worldwide, and the WHO estimated in 2024 that 50 million people were chronically infected with the virus [53].
Two FDA-approved drugs targeting the HCV non-structural (NS) proteins NS3/4a protease were developed using computational methods. NS3 is a non-structural protein with two domains: N-terminal serine protease and C-terminal RNA helicase [55]. NS4a is a polypeptide co-factor for the protease activity of NS3. The NS3/4a complex processes the HCV polyprotein, releasing among the cleavage products, the non-structural proteins required for virus replica­tion [56]. HCV is phylogenetically classied into eight genotypes, named 1 to 8,
15 Molecular Modeling Strategies in Drug Design, Development, and... 445
Fig. 15.5 Structure-based development of grazoprevir. Chemical representation of BILN-2061 (a); crystal structure of the full-length NS3/4A (protease domain with residues in green; helicase domain with residues in pink, the enzyme is colored in gray) (PDB ID: 1CU1) (b); and chemical structure of grazoprevir (c). The P4–P1 positions of each compound are labeled. Important residues and the compounds are represented as sticks and colored by atom. (Figure produced using ChemDraw and PyMOL)
according to the date when they were discovered [57]. Most of the hepatitis C cases involve GT1 (44%), GT3 (25%), and GT4 (15%) [58]. The rst drugs developed targeted GT1, and as the other genotypes were being described, resistance emer ged, making necessary the genotyping of patientssamples to select the best treatment option; however, this was only sometimes possible. Thus, the discovery of pan-genotypic anti-HCV compounds represented a signicant advance in hepatitis C treatment, and nowadays, these compounds are used across the globe, and the countries adopting them are released from the need for sample genotyping [59 ].
The development of grazoprevir and voxilaprevir will be discussed here and they have the same starting point. The rst macrocyclic inhibitors designed were based on NMR data of subst rate-like peptide inhibitors of NS3/4a protease and were rigid to ensure the trans geometry of the P2-P3 amide bond [60]. Later, the macrocyclic inhibitor BILN-2061 (Fig. 15.5a) was modeled into the active site of the apo crystal structure of NS3/4a protease (PDB ID 1CU1) [61, 62]. Considering that the P2 and thiazolyl quinoline portions of BILN-2061 lie on pockets formed between the protease and helicase domains of NS3/4a, more analogs were designed and modeled to the same crystal structure. This modeling led to the design of compounds with a P2–P4 macrocyclic constraint active against genotypes GT1 and GT2 of NS3/4a protease [63]. However, analogs with a large substituent to the P2 heterocycle and fused ring were more active against the GT3 genotype enzyme when compared to GT1. After modeling these analogs [14], a cyclopropyl constraint was added to the P2–P4 macrocyclic linker, improving the electrostatic interactions with the residue 156 (Fig. 15.5b), probably leaving room to accommodate the A156T/V substitutions observed in resistant HCV populations, also resulting in increased the lipophilicity to enhance the liver exposure (since HCV infects the liver), and a quinoxaline was added to improve the compound’s solubility. All of these resulted in the discovery of grazoprevir (Fig. 15.5c), approved in 2016 by the FDA under the name Zepartier
®
,a
single-oral dose pill also containing the NS5a inhibitor elbasvir [64].
446 V. C. Santos et al.
Fig. 15.6 Structure-based development of voxilaprevir. Chemical representations of compound 3 and voxilaprevir (a). Crystal structure of voxilaprevir complexed with GT1 D168Q (GT3
surrogate) NS3/4A protease (PDB ID 6NZT) (b). Water molecules are represented as red spheres, and the polar contacts are shown in yellow dashed lines. The P4–P1 positions of each compound are labeled. Important residues and compounds are represented as sticks and colored by atom. Carbons are colored gray in the enzyme and green in the compound. (Figure produced using ChemDraw and PyMOL)
Patients treated with grazoprevir had their serum alanine transaminase elevated, a potential biomarker for hepatotoxicity, resulting in a reduction in the clinical dosage and warnings on the prescription label [15]. Another issue that emerged with the description of new HCV genotypes was that grazoprevir shows higher activity against GT1 than GT3 [65]. Therefore, researchers focused on improving the activity of the molecules against HCV genotypes targeting the catalytic triad residues (Ser139, His57, and Asp81) since they are conserved across the genotypes. This led to the developed of compound 3 (Fig. 15.6a), with good antiviral [half-maximal effective concentration (EC
) of 23 nM] and enzymatic (Kiof 165 pM) potency. An
50
X-ray crystallography structure of compound 3 with GT1 D168Q (GT3 surrogate) NS3/4A protease (PDB ID 6NZV) showed the ethyl part of 3 in a van der Waals interaction with His57.
Additionally to the improvements in potency against GT3, efforts were made to improve the compounds pharmacokinetics and liver distribution to reduce the hepatotoxicity. The search for compounds with superior metabolic stability and reduced formation of protein adducts eventually led to the development of voxilaprevir (Fig. 15.6a)[15, 66]. Voxilaprevir is more potent than 3 in GT3 enzymatic (K
of 63 pM) and antiviral (EC50of 6.1 nM) assays. This higher potency
i
might be explained by hydrophobic contact between the diuoro methylene on the macrocycle and the alkyl portion of R155, as observed in the co-crystal with GT1
15 Molecular Modeling Strategies in Drug Design, Development, and... 447
D168Q (GT3 surrogate) NS3/4A protease (PDB ID 6NZT) (Fig. 15.6b). Overall, the activity of Voxilaprevir against common GT1–6 ranged between an EC
6.6 nM. Voxilaprevir, together with sofosbuvir (inhibitor of the HCV NS5B poly­merase) and velpatasvir (HCV NS5A inhibitor), is a component of Vosevi
of 1.5 and
50
®
approved in 2017 as a pan-genotypic treatment for patients who failed previous therapies for hepatitis C [15].
,
4 Structure-Based Drug Design of Nirmatrelvir
pro
and Ensitrelvir as SARS-CoV-2 M
Since 2020, in response to the COVID-19 pandemic, there have been remarkable efforts to design drugs targeting proteases. The description of COVID-19 was quickly followed by the identication of its causing agent, the severe acute respira­tory syndrome-related Coronavirus 2 (SARS-CoV-2), which was classied in the Coronaviridae family by the Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, based on the recognized similarity to bat coronaviruses and human coronaviruses [67]. The rst cases of the disease were reported initially as pneumonia of unknown origin, in November 2019, in Wuhan (China). Just 4 months later, in March 2020, COVID-19 had spread throughout the globe, and a pandemic situation was declared. By that point, the SARS-CoV-2 genome had been sequenced [ 68 ], revealing high similarity to other coronaviruses, and there were already crystallographic structures of SARS-CoV-2 main protease
pro
(M
, also known as chymotrypsin-like protease, 3CL
like protease (PL
pro
M
and PL viral polypeptides pp1a and pp1ab into 16 nonstructural viral proteins [70]. Thus, these proteases were promptly targeted for drug design. Later, with a better under­standing of the process of host cell infection by SARS-CoV-2, the human proteases Cathepsin L and TMPRSS2 were also identied as targets for the development of COVID-19 treatments [71, 72 ]. While there are numerous studies on each of these four targe t proteases, the most successfully targeted is M our discussion on this target. In addition to its importance for viral replication, M is considered a good drug target due to its unique specicity for Gln at P1, which is not found among human cysteine proteases, contributing to the developing specic
pro
M
inhibitors and improves drug safety. Also, its conser vation among coronavirus
creates the potential for developing broad-spectrum antiviral drugs.
Computational strategies employed toward the development of M include docking-based virtual screening of FDA-approved drugs [73], in-house libraries [74, 75], and ultra-large commercial libraries [76, 77] (see Chaps. 8 and 11). Free energy perturbation calculations (see Chap. 10) have also led to potent
pro
M
inhibitors with antiviral activity [78]. Machine learning models have also been
successfully employed to extract information from high-throughput structural data
pro
) deposited in the Protein Data Bank.
pro
are essential for SARS-CoV-2 multiplication, as they process the
Inhibitors
pro
, or NS5) [69 ] and papain-
pro
, and thus we will focus
pro
pro
inhibitors
448 V. C. Santos et al.
Fig. 15.7 Structure-based development of nirmatrelvir. Chemical structures of the PF-00835231 (lead compound) and PF-07321332 (nirmatrelvir) (a). Binding mode of nirmatrelvir (PDB ID: 7RFW) in the SARS-CoV-2 M lines. The P4–P1 positions of each compound are labeled. Important residues and compounds are represented as sticks and colored by atom. Carbons are colored gray in the enzyme and salmon in the compound. (Figure produced using ChemDraw and PyMOL)
pro
active site (b). Hydrogen bonds are represented as yellow dashed
and benet the design of inhibitors that reveal potent antiviral properties [79]. Alto­gether, efforts based on computer-aided techniques and experimental approaches have yielded several class es of M
pro
inhibitors (reviewed by [ 80]), including
marketed drugs.
The active site conservation between SARS-CoV and SARS-CoV-2 was a key factor contributing to the quick development of Paxlovid the SARS-CoV-2 M developing nirmatrelvir was the SARS-CoV M
pro
inhibitor nirmatrelvir and ritonavir. The starting point for
pro
®
, a medicine containing
inhibitor PF-00835231, previ­ously developed in structure-based design efforts against SARS-CoV [81]. After the outbreak of COVID-19, PF-00835231 was also shown to be potent against the SARS-CoV-2 enzyme and in infected Vero E6 cells, showing stability in plasma, adequate solubility, and clearance rates suitable for development as a COVID-19 treatment via intravenous infusion [81].
Nevertheless, the low passive absorptive permeability of PF-00835231 was an important limitation that had to be overcome to obtain an orally administered drug. Thus, PF-00835231 was the lead compound for structure-based efforts to optimize its pharmacokinetic properties (Fig. 15.7a). Throughout optimization, molecular modeling studies against SARS-CoV-2 M
pro
were employed to suggest compounds that should simultaneously result in favorable pharmacokinetic properties and main­tain high potency against the target [12]. Examples of modications guided by modeling studies include the removal of hydrogen bond donors to improve oral absorption and the incorporation of a nitrile warhead to enhance solubility while also introducing modications to ensure the occupation of the S2 and S3 pockets and performing hydrogen bond interactions with Gln189 and Glu166 (Fig. 15.7b, c).
15 Molecular Modeling Strategies in Drug Design, Development, and... 449
Among the compounds developed, PF-07321332 (nirmatrelv ir) was chosen as the clinical candidate considering its potent activity against M
pro
, in antiviral assays and animal models, the ease of synthetic scale-up, reduced propensity for epimerization, and enhanced solubility. Additionally, it showed antiviral activity against multiple coronaviruses and no inhibitory effects against a wide panel of mammalian pro­teases, G protein-coupled receptors, kinases, transporters, phospho diesterases, and cardiac ion channels. One limitation in nirmatrelvirs prole was its intense metab­olism by CYP450, especially by CYP3A4. To overcome this hurdle, co-administration with ritonavir, a potent CYP3A4 inhibitor, was proposed and yielded an improved pharmacokinetic prole [12]. This combination demonstrates how CYP450 inhibition, frequently considered an unfavorable property due to associated drug–drug interactions, was explored positively. The nirmatrelvir/ritona­vir combination, licensed as Paxlovid
®
, reduced hospitalization by 89% in unvaccinated adults at high risk for progression to severe COVID-19 [82]. Paxlovid was approved for emergency use by the FDA in December 2021, followed by approval by several international agencies, and was fully approved in May 2023.
The development of ensitrelvir (Xocova structure-based approaches [13]. Aiming to discover noncovalent and nonpeptidic inhibitors of SARS-CoV-2 M
pro
, researchers performed a docking-based virtual
®
) was also highly supported by
screening of their in-house library. To lter the docking results, they also built a pharmacophoric model based on the crystallographic structures of three ligands in complex with M
pro
. The pharmacophore consisted of an acceptor site hydrogen bonding with the side-chain NH donor of His163 in S1, a lipophilic site in S2, and an acceptor site interacti ng with the Glu166 main-chain NH, all of which had to be present. It is interesting to highlight that the denition of a pharmacophore was supported by the large amount of structural data of complexes of ligands bound to
pro
M
, including those from important initiatives such as the COVID-19 Moonshot [83]. After ltering to ensure the compounds met the proposed pharmacophore, the top 300 compounds from the virtual screening were evaluated in biochemical assays with M optimization. While 4 had a moderate potency against the enzyme (IC
pro
. Among the hits with IC50under 10 μM, hit 4 was prioritized for
of
50
8.6 μM), it presented a favorable pharmacokinetic prole with in vitro metabolic stability, high oral bioavailability, and low clearance in vivo in rats. Co-crystallization of 4 with M
pro
conrmed the binding mode predicted by docking and supported its structure-based optimization based on modications in two regions (Fig. 15.8a, b). First, to optimize interactions with the S1pocket, a cyclization was performed in the P1motif while maintaining the hydrogen bond with Thr26, resulting in compound 5. Remarkably, a 90-fold improvement in enzymatic inhibi­tion (IC
of 0.096 μM) was obtained with this modication while keeping a
50
favorable pharmacokinetic prole. Then, ensitrelvir (a.k.a. S-217622) was designed by an additional cyclization in the P1 motif and a modication in the pattern of uorine substitution in the P2 ring (Fig. 15.8a, c). Ensitrelvir showed high potency against M
pro
(IC50of 0.013 μM) and in antiviral assays (EC50of 0.37 μM), high metabolic stability in vitro, high oral absorption, and low clearance in rats, monkeys, and dogs.
®