Small-Molecule Inhibitors of HIV-1 Protease Dimerization Derived from Cross-Linked Interfacial Peptides (original) (raw)
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HIV & AIDS Review
Introduction: Human immunodeficiency virus (HIV) protease enzyme is one of the most promising therapeutic targets for acquired immunodeficiency syndrome (AIDS) treatment. Due to mutation of the virus, there is always a room for new agents. Material and methods: The aim of in silico molecular docking study was to analyze and compare the binding mode of seven Food and Drug Administration (FDA)-approved HIV protease enzyme inhibitors, and to understand their structural requirements to inhibit an enzyme by using Schrodinger model as well as to evaluate a free energy of binding of these inhibitors with an enzyme. Results: The binding mode analysis showed that the active site was present at the interface of two chains A and B of the enzyme and the crucial amino acid remained responsible for the binding of inhibitors to the HIV-1 protease, which could help to classify the inhibitors as better drug targets. Results of this comparative binding mode analysis of seven FDA-approved drugs could be potential and useful for designing of a new effective inhibitor of HIV-1 protease. Out of seven inhibitors drugs, only two drugs present the best inhibition. HIV protease-nelfinavir complex with PDB: 2Q64 and HIV protease D30N, and R41A double mutant-tipranavir complex in PDB: 1D4S double mutant V82F and I84V, were used as templates for applying the mutations on HIV protease active site. Furthermore, the structure-based computer-assisted search for the comparison of the two inhibitors of HIV protease was completed. On the other hand, tipranavir seems to be a broad specificity inhibitor, as no changes in the bond lengths with the introduction of mutations were observed. Conclusions: Tipranavir could be targeted more effectively for designing future drug analogues, as it is less vulnerable to mutations. HIV mutants reported in this study could also be used for preliminary identification of specific inhibitors, as drugs that may alter the HIV protease activity for medicinal use.
Biochemical Society Transactions, 2007
Mutations that occur in response to the HIV-1 protease inhibitors are responsible for the development of multidrug cross-resistance to these antiproteases in AIDS treatment. One alternative to inhibiting the active site of HIV-1 protease is to target the dimer interface of the homodimeric enzyme at the antiparallel β-sheet formed by the interdigitation of the C- and N-ends of each monomer. This region is highly conserved and is responsible for approx. 75% of the dimer-stabilization energy. The strategies that have been used to design small molecules to target the interface antiparallel β-sheet have produced lipopeptides, guanidinium derivatives and peptides (or peptidomimetics) cross-linked with spacers. The mechanism of inhibition was determined using a combination of kinetic and biophysical methods. These dimerization inhibitors proved equally active in vitro against both wild-type and mutated proteases. They are therefore promising alternatives to active-site-directed inhibitors ...
INHIBITORS OF HIV-1 PROTEASE: A Major Success of Structure-Assisted Drug Design 1
Annual Review of Biophysics and Biomolecular Structure, 1998
Retroviral protease (PR) from the human immunodeficiency virus type 1 (HIV-1) was identified over a decade ago as a potential target for structure-based drug design. This effort was very successful. Four drugs are already approved, and others are undergoing clinical trials. The techniques utilized in this remarkable example of structure-assisted drug design included crystallography, NMR, computational studies, and advanced chemical synthesis. The development of these drugs is discussed in detail. Other approaches to designing HIV-1 PR inhibitors, based on the concepts of symmetry and on the replacement of a water molecule that had been found tetrahedrally coordinated between the enzyme and the inhibitors, are also discussed. The emergence of drug-induced mutations of HIV-1 PR leads to rapid loss of potency of the existing drugs and to the need to continue the development process. The structural basis of drug resistance and the ways of overcoming this phenomenon are mentioned.
Two-step binding mechanism for HIV protease inhibitors
Biochemistry, 1992
Rate constants for binding of five inhibitors of human immunodeficiency virus (HIV) protease were determined by stopped-flow spectrofluorometry. The two isomers of quinoline-2-carbonyl-Asn-PheW [ CH(OH)CHzN]Pro-0-t-Bu (R diastereomer = 1R; S diastereomer = 1s) quenched the protein fluorescence of HIV protease and thus provided a spectrofluorometric method to determine their binding rate constants. The dissociation rate constants for acetyl-Thr-Ile-Leu\k(CHzNH)Leu-Gln-Arg-NHz (2), (carbobenzyloxy)-P~~*[CH(OH)CHZN]P~O-O-~-BU (3), and pepstatin were determined by trapping free enzyme with 1R as 2,3, and pepstatin dissociated from the respective enzyme-inhibitor complex. Association rate constants of lR, 2, and pepstatin were calculated from the time-dependent inhibition of protease-catalyzed hydrolysis of the fluorescent substrate (2-aminobenzoyl)-Thr-Ile-Nle-Phe(NO~)-Gln-Arg-NH~ (4). The kinetic data for binding of 1s to the protease fit a two-step mechanism. Kd values for these inhibitors were calculated from the rate constants for binding and were similar to the respective steady-state Ki values. Human immunodeficiency virus (HIV) * protease is a 22-kDa dimer of two identical 11-kDa subunits (Meek et al., 1989). The protease maturation from the gag-pol polyproteingeneproduct is autocatalytic (Deboucket al., 1987). Since the protease is required for maturation of infectious HIV particles (Kohl et al., 1988; Peng et al., 1989; Gottlinger et al., 1989), it is a potential target for chemotherapeutic treatment of AIDS. Numerous peptide-based inhibitors and nonpeptide inhibitors have been synthesized [recently reviewed by Huff (1991) and Norbeck and Kempf (1991)l. Some of these compounds inhibit maturation of viral particles in vitro
Discovery and optimization of nonpeptide HIV-1 protease inhibitors
Bioorganic & Medicinal Chemistry, 1996
Several small, achiral nonpeptide inhibitors of H1V-I protease with low micromolar activity were identified by mass screening of the Parke-Davis compound library. Two of the compounds, structurally similar, were both found to be competitive and reversible inhibitors [compound 1, 4-hydroxy-3-(3-phenoxypropyl)-l-benzopyran-2-one: K, = 1.0 p.M; compound 2, 4-hydroxy-6-phenyl-3-(phenylthio)-pyran-2-one: K~ = 1.1 ~tM]. These inhibitors were chosen as initial leads for optimization of in vitro inhibitory activity based on molecular modeling and X-ray crystallographic structural data. While improvements in inhibitory potency were small with analogues of compound 1, important X-ray crystallographic structural information of the enzyme-inhibitor complex was gained. When bound, 1 was found to displace H20301 in the active site while hydrogen bonding to the catalytic Asps and Ile50 and Ilel50. "[he pyranone group of compound 2 was found to bind at the active site in the same manner, with the 6-phenyl and the 3-phenylthio occupying P1 and PI', respectively. The structural information was used to develop design strategies to reach three or four of the internal pockets, P2-P2'. This work led to analogues of diverse structure with high potency (IC50 < 10 nM) that contain either one or no chiral centers and remain nonpeptidic. The highly potent compounds possess less anti-HIV activity in cellular assays than expected, and current optimization now focuses on increasing cellular activity. The value of the HIV-1 protease inhibitors described is their potential as better pharmacological agents with a different,pattern of viral resistance development, relative to the peptidic inhibitors in human clinical trials.
Biochemistry, 1994
2R,4S,5S,1'S)-2-Phenylmethyl-4-hydroxy-5-(fe~f-butoxycarbonyl)amino-6-phenylhexanoyl-N-( l'-imidaz0-2-y1)-2'-methylpropanamide (compound 2) is a tripeptide analogue inhibitor of HIV-1 protease in which a C-terminal imidazole substituent constitutes an isoelectronic, structural mimic of a carboxamide group. Compound 2 is a potent inhibitor of the protease (Ki = 18 nM) and inhibits HIV-1 acute infectivity of CD4+ T-lymphocytes (ICs0 = 570 nM). Crystallographic analysis of an HIV-1 protease-compound 2 complex demonstrates that the nitrogen atoms of the imidazole ring assume the same hydrogen-bonding interactions with the protease as amide linkages in other peptide analogue inhibitors. The sole substitution of the C-terminal carboxamide of a hydroxyethylene-containing tripeptide analogue with an imidazole group imparts greatly improved pharmacokinetic and oral bioavailability properties on the compound compared to its carboxamide-containing homologue (compound 1). While the oral bioavailability of compound 1 in rats was negligible, compound 2 displayed oral bioavailabilities of 30% and 14%, respectively, in rats and monkeys.
Current Opinion in HIV and AIDS, 2008
Purpose of reviewDrug resistance occurs as a result when the balance between the binding of inhibitors and the turnover of substrates is perturbed in favor of the substrates. Resistance is quite wide spread to the HIV-1 protease inhibitors permitting the protease to process its ten different substrates. This processing of the substrates permits the HIV-1 virus to mature and become infectious. Designing HIV-1 protease inhibitors that closely fit within the substrate binding region is proposed to be a strategy to avoid drug resistance.Recent findingsCo-crystal structures of HIV-1 protease with its substrates define an overlapping substrate binding region, or substrate envelope. Novel HIV-1 protease inhibitors that were designed to fit within this substrate envelope, were found to retain high binding affinity and have a flat binding profile against a panel of drug resistant HIV-1 proteases.SummaryAvoiding drug resistance needs to be considered in the initial design of inhibitors to quickly evolving targets such as HIV-1 protease. Using a detailed knowledge of substrate binding appears to be a promising strategy for achieving this goal to obtain robust HIV-1 protease inhibitors.
Biochemistry, 2009
Wild-type and drug-resistant mutated HIV-1 proteases are active as dimers. This work describes the inhibition of their dimerization by a new series of alkyl tripeptides that target the four-stranded antiparallel -sheet formed by the interdigitation of the N-and C-monomer ends of each monomer. Analytical ultracentrifugation was used to give experimental evidence of their mode of action that is disruption of the active homodimer with formation of inactive monomer-inhibitor complexes. The minimum length of the alkyl chain needed to inhibit dimerization was established. Sequence variations led to a most potent HIV-PR dimerization inhibitor: palmitoyl-Leu-Glu-Tyr (K id ) 0.3 nM). Insertion of D-amino acids at the first two positions of the peptide moiety increased the inhibitor resistance to proteolysis without abolishing the inhibitory effect. Molecular dynamics simulations of the inhibitor series complexed with wild-type and mutated HIV-PR monomers corroborated the kinetic data. They suggested that the lipopeptide peptide moiety replaces the middle strand in the highly conserved intermolecular four-stranded -sheet formed by the peptide termini of each monomer, and the alkyl chain is tightly grasped by the active site groove capped by the -hairpin flap in a "superclosed" conformation. These new inhibitors were equally active in Vitro against both wild-type and drug-resistant multimutated proteases, and the model suggested that the mutations in the monomer did not interfere with the inhibitor.
2016
Drug resistance mutations in HIV-1 protease selectively alter inhibitor binding without significantly affecting substrate recognition and cleavage. This alteration in molecular recognition led us to develop the substrateenvelope hypothesis which predicts that HIV-1 protease inhibitors that fit within the overlapping consensus volume of the substrates are less likely to be susceptible to drug-resistant mutations, as a mutation impacting such inhibitors would simultaneously impact the processing of substrates. To evaluate this hypothesis, over 130 HIV-1 protease inhibitors were designed and synthesized using three different approaches with and without substrate-envelope constraints. A subset of 16 representative inhibitors with binding affinities to wild-type protease ranging from 58 nM to 0.8 pM was chosen for crystallographic analysis. The inhibitor-protease complexes revealed that tightly binding inhibitors (at the picomolar level of affinity) appear to "lock" into the protease active site by forming hydrogen bonds to particular active-site residues. Both this hydrogen bonding pattern and subtle variations in protein-ligand van der Waals interactions distinguish nanomolar from picomolar inhibitors. In general, inhibitors that fit within the substrate envelope, regardless of whether they are picomolar or nanomolar, have flatter profiles with respect to drug-resistant protease variants than inhibitors that protrude beyond the substrate envelope; this provides a strong rationale for incorporating substrate-envelope constraints into structure-based design strategies to develop new HIV-1 protease inhibitors.