Patent Grant
9404142
The invention relates to the field of parasitology. More particularly, it relates to the identification of inhibitors of Plasmodium, and to screening methods for identifying such inhibitors.
Malaria is the most important human parasitic disease. More than forty percent of the world's population live in areas where malaria is transmitted (e.g., parts of Africa, Asia, the Middle East, Central and South America, Hispaniola, and Oceania). An estimated 700,000-2.7 million persons die of malaria each year, 75% of them being African children.
Biochemical and genetic analyses have shown that proteases of Plasmodium, the causative agent of malaria, play a central role in the entrance of the sporozoite and the merozoite into the host hepatocyte or red blood cell (RBC), respectively. The surface proteins of both extracellular invasive forms undergo obligatory proteolytic processing executed by parasite-encoded serine proteases, which are thus directly accessible to host factors such as antibodies or drugs. Importantly, 60% of the plasmatic proteins are protease inhibitors (mainly involved in the regulation of coagulation or complement activation) suggesting that the parasitic proteases active on the outer surface of the parasite are highly specific, differ from the host proteases and are insentive to host plasmatic protease inhibitors. Altogether, the features of the parasite serine proteases involved in RBC and hepatocytes invasion make them attractive targets as novel anti-malarials.
SUB2 and SUB1 are two essential Plasmodium serine proteases which are known to be involved in host cells invasion. The SUB2 subtilisin-like serine protease is discharged by the parasite onto the surface of the extracellular merozoite, where it performs proteolytic processing of major parasite surface proteins, a final maturation step that is essential for host cell invasion. SUB2 sequence is highly conserved in P. falciparum and P. vivax. Because of all its interesting properties, SUB2 has been described as a novel anti-malarial drug target in International PCT patent application WO2006/120579. The SUB1 enzyme has been shown to be involved in the egress of Plasmodium from infected erythrocytes and plays also a yet undefined role during the RBC invasion process per se. The SUB1 enzyme of P. falciparum has also been the subject of a fluorescence-based assay for identifying inhibitors of P. falciparum (Blackman et al. (2002), Biochemistry, 41, 12244-12252). SUB2 and SUB1 share substantial inter-species structural homology in their catalytic domains (e.g. >75% sequence identity between the PfSUB2 and PvSUB2 domains, and between PfSUB1 and PvSUB1 domains). The Plasmodium genome harbours a third prokaryotic subtilisin-like serine protease, SUB3, which differs from SUB1 and SUB2 in being not essential for the intra-erythrocytic cycle. However, its expression is activated after the entry of the sporozoites into the hepatocytes, suggesting a role during the establishment of the infectious process in mammalian hosts.
Chloroquine is a 4-aminoquinoline drug used in the treatment or prevention of malaria. Popular drugs based on chloroquine phosphate (also called nivaquine) are Chloroquine FNA, Resochin and Dawaquin. Worryingly, resistance to both Plasmodium falciparum and P. vivax, the two main species infecting humans, have eroded treatment efficacy and malaria control measures. In addition, mosquito resistance to insecticides is spreading. Efforts at developing a malaria vaccine with long term efficiency have met with limited success.
There is thus an urgent need for the discovery, screening and development of novel anti-malarials. There is also a need for compounds targeting Plasmodium invasion process of either the hepatocyte or the red blood cells. There is also a need for enzyme inhibitors effective for prophylaxis preventing host infection.
The present inventors have designed methods for screening inhibitors of Plasmodium, and more particularly inhibitors of Plasmodium subtilisin-like proteases. The inventors have also identified new inhibitors of Plasmodium, and more particularly inhibitors of Plasmodium subtilisin-like proteases.
One particular aspect of the invention relates to a screening method for identifying inhibitors of Plasmodium and compounds identified using such methods, including more particularly inhibitors of Plasmodium subtilisin-like proteases. The screening method of the invention can be a low throughput screening or a high throughput screening. Alternatively, the screening method of the invention can comprise one or several step(s) of low throughput screening and one or several step(s) of high throughput screening.
A related aspect concerns tagged peptidic substrates for use in screening assays directed in indentifying inhibitors of Plasmodium. The tagged peptidic substrates may be particularly useful in high-throughput screening methods and screening assays. Related aspect concerns high-throughput screening methods, including fluorescence based methods comprising the use of such tagged peptidic substrates for identifying inhibitors of Plasmodium, including inhibitors of Plasmodium subtilisin-like proteases.
The invention also relates to methods for identifying compounds capable of targeting more than one protease, presumably at different parasite stages, which is likely to maximize efficacy, and minimize the risks of failure or resistance. In other embodiments, the selected Plasmodium proteases belong to the same family of enzymes, thus displaying common features in their active sites, thereby providing the possibility of identifying biologically active inhibitors capable of binding multiple Plasmodium targets. The methods of the invention may also be useful in identifying anti-malarial candidates targeting a set of Plasmodium enzymes crucial for the parasite invasion into and egress from host cells processes.
The invention also relates to nucleic and amino acid sequences as shown in
The invention further encompasses assay kits and methods for screening of possible therapeutic anti-malaria compounds and compositions to help alleviate, treat and/or prevent Plasmodium infections, especially in humans.
Additional aspects, advantages and features of the present invention will become more fully understood from the detailed description given herein and from the accompanying drawings, which are exemplary and should not be interpreted as limiting the scope of the invention.
I. Screening Methods
One aspect of the invention concerns screening methods for identifying inhibitors of Plasmodium, and more particularly inhibitors of Plasmodium subtilisin-like proteases. In the context of the present invention, “inhibitors of Plasmodium” or “anti-malaria compounds” refer to compounds that are able to help alleviate, treat and/or prevent Plasmodium infections, especially in humans. Suitable inhibitors according to the invention include those compounds capable of inhibiting Plasmodium life-cycle, including but not limited to inhibition of Plasmodium growth, multiplication, development, liberation from host-infected cells and invasion into host cells. In some embodiments, these compounds are able to inhibit the parasite invasion into and egress from red blood cells. In some embodiments, the compounds are inhibitors of Plasmodium subtilisin-like proteases, able to inhibit the enzymatic activity of a Plasmodium subtilisin-like serine protease. Preferably, the compounds are inhibitors of orthologous subtilisin-like serine protease (i.e. “same” or “corresponding” protease from different Plasmodium species). In other preferred embodiments, the compounds are inhibitors of different types subtilisin-like serine protease (e.g. SUB1, SUB2 and SUB3).
In Vitro Screening of Plasmodium Inhibitors
According to additional particular aspects, the invention relates to in vitro screening methods and tagged peptidic substrates for identifying inhibitors of Plasmodium. These in vitro screening methods and substrates are based on the importance of normal biological activity of subtilisin-like proteases for the life-cycle of various species of Plasmodium such as Plasmodium vivax, Plasmodium falciparum, Plasmodium berghei and other Plasmodium species. Potentially pharmaceutically useful inhibitors of Plasmodium can thus be identified by measuring the effect of candidate compounds on one or more subtilisin-like proteases. Accordingly, the present inventors have developed tagged peptidic substrates and related methods for measuring subtilisin-like proteases activity.
In one embodiment, the in vitro screening method for identifying inhibitors of Plasmodium, comprises assessing cleavage of a peptidic substrate in presence of a candidate compound, wherein the peptidic substrate is cleavable by a protease comprising SEQ ID NO: 4. A particular example of a protease comprising SEQ ID NO: 4 is the active form of PvSUB1-Belem which amino acid sequence is illustrated in
In a preferred embodiment, the tagged peptidic substrate comprises two aspartic acids and the protease cleaves the peptidic substrate between these two aspartic acids. Preferably the tagged peptidic substrate comprises the amino acid sequence K-L-V-G-A-D-D-V-S-L-A (SEQ ID NO: 9). In another embodiment, the tagged peptidic substrate comprises the amino acid sequence K-L-V-G-A-D-D-V-S-L-A-K (SEQ ID NO: 10).
As it will be exemplified hereinafter, the peptidic substrate is preferably tagged with a quencher and/or a fluorophore, most preferably both, for easily measuring cleavage of the peptide in high-throughput fluorescence assays such as FRET. Examples of suitable quenchers include, but are not limited to, Dabsyl and DYQ60. Examples of suitable fluorophores include, but are not limited to, EDANS or DY630. Because they allow screening a large diversity of chemical compounds in an enzymatic assay in a robust and reproducible way, the following combinations of quencher and fluorophore are preferred: i) Dabsyl and EDANS; and ii) in a most preferred way DYQ660 and DY630, which work with excitation and emission wavelengths in the far red spectrum, thus reducing the risks of auto-fluorescence of the chemical compounds. In preferred embodiments, the tagged peptidic substrate consists of Dabsyl-K-L-V-G-A-D-D-V-S-L-A-EDANS (Dabsvl-SEQ ID NO: 9-EDANS) or DYQ660-K-L-V-G-A-D-D-V-S-L-A-K-DY630 (DYQ660-SEQ ID NO: 10-DY630). It is within the skill of those in the art to select suitable quenchers and fluorophores and other possibilities include for instance Dabcyl and EDANS, 5-IATR, 6-IATR.
In particular embodiments, the in vitro screening method comprises assessing cleavage of the peptidic substrate in presence and in absence of a candidate compound. Accordingly a candidate compound is considered an inhibitor of Plasmodium if the cleavage of the peptidic substrate is reduced when compared to testing under similar conditions, in the absence of the candidate compound.
Inhibitory activity of the candidate compound may also be quantified. For instance, the in vitro testing may comprise: (i) measuring an inhibition constant (Ki) for the one or more Plasmodium subtilisin-like protease in presence of the candidate compound and/or (ii) measuring a half maximal inhibitory concentration (IC50) of the candidate compound on the one or more Plasmodium subtilisin-like protease. In particular embodiments, compounds having a Ki lower than about 50 μM, lower than 25 μM, lower than 10 μm, or lower than 5 μM may be considered interesting candidates and selected for further testing and development.
Preferably, the in vitro screening method of the invention is a high-throughput method. Suitable methods include fluorescence-based methods such as Fluorescent Resonance Energy Transfer (FRET). Those skilled in the art are capable of indentifying additional high-throughput methods, techniques and assays which can be adapted for screening and/or identifying inhibitors of Plasmodium, and/or for assessing cleavage of a peptidic substrate according the methods of the invention.
The in vitro screening method of the invention may comprise additional steps for selecting, validating or chemically optimizing potentially useful candidate compounds. Potentially active inhibitors may thus be tested in any suitable in silico, in vitro, ex vivo and/or in vivo assays. In a particular embodiment the in vitro screening method further comprises selecting a candidate compound capable of inhibiting cleavage of the peptidic substrate; and testing the selected compound ex vivo on a culture of one or more species of Plasmodium and/or testing said selected compound in vivo in at least one Plasmodium-infected animal. Although it is generally preferable to proceed incrementally from in silico, in vitro, ex vivo to in vivo testing, the invention is not limited to a particular order.
In Silico Screening of Plasmodium Inhibitors
The invention further relates to computational related methods for screening and/or identifying inhibitors of Plasmodium in silico.
According to a particular aspect, the invention relates to a screening method for identifying inhibitors of Plasmodium, comprising:
In one particular embodiment, the screening method comprises:
According to another aspect, the invention relates to a screening method for identifying inhibitors of multiple Plasmodium species. In one embodiment the method comprises:
In a further aspect, the invention relates to a method for identifying inhibitors of multiple Plasmodium species, comprising testing with at least two different techniques for candidate compounds having a desired Plasmodium protease inhibitory or binding activity;
The screening methods above comprise a step that is carried out in silico. In silico screening of drugs and in silico-based drug design is becoming more and more popular (e.g. Song et al., 2005, PNAS, 102:4700-05; Plewczynski et al., 2007, Chem Biol Drug Des, 69:269-279; Leitao et al., 2008, Eur J Med Chem, 43:1412-1422; Kirchmair et al, 2008, Curr Med Chem 15:2040-53; Zoete et al., 2009, J Cell Mol Med, 13:238-78; Jain A N 2004, Curr Opin Drug Discov Devel, 7:396-403; Rester U 2008, Curr Opin Drug Discov. Devel 11:559-68). The present invention uses general principles of in silico screening known and applied by those skilled in the art in the discovery or screening of enzymes inhibitors, including protease inhibitors. Without being bound by any particular details or explanation, a first element which is typically required is a virtual 3D-structure of the targeted protein. Such structure may be obtained from the 3D X-ray crystallography resolution, or from a model deriving from the 3D X-ray crystallography resolved structure of one or more closely related proteins. The second required element is a precise spatial identification of the catalytic site of interest (e.g. hydrophobic pocket). Such precise spatial identification generally comprises 3D coordinates of (i) the catalytic site where the substrate will dock and (ii) of the proximal amino acids which participates in the docking because of physico-chemical forces (e.g. hydrophobic interactions, hydrogen bonding, van der Waals forces, etc.). Finally, the third required element is the 3D structure of the chemical compounds to be tested (e.g. a library of chemical compounds). 3D structure of a chemical compound may be a X-ray crystallography resolved structure or a 3D structure which has been modeled using the 2D chemical structure or the chemical formula of the compound. Having these three elements in silico screening typically takes place by using computational chemistry software, the software calculating, for each chemical compound to be tested, probabilities for the compound to interact or bond into the catalytic site of the targeted protein. Compounds with the best score are selected for subsequent in vitro, ex vivo, and/or in vivo rounds of screening. Suitable computational chemistry software include, but are not limited to, Flex™, FlexX-Pharm™, and Icm™.
The Plasmodium protease may be selected from the subtilisin-like protease 1 “SUB1”, the subtilisin-like protease 2 “SUB2”, and the subtilisin-like protease 3 “SUB3”. One may take advantage of the similarity of Plasmodium subtilisins active site and use, as the 3D model, a homology model of two different Plasmodium proteases (e.g. SUB1 and SUB2). Similarly, one may take advantage of the similarity of SUB1 active site with bacterial subtilisins and use, as the 3D model, a homology model based on known bacterial and/or fungi subtilisins 3D structures. Examples of known and accessible 3D structures include, but are not limited to, those published in the RCSB Protein Data Bank™ that are directly accessible on the web site pdb.org or via the NCBI web site. Particular examples include the following proteins: BPN′ (Acc. No. 1LW6); sphericase (Acc. No. 1EA7); Thermitase (Acc. No. 2TEC); AK-1 Serine protease (Acc. No. 1 DBI); subtilisin Carlsberg (Acc. No. 1ROR); proteinase K (Acc. No. 1106) and Bacillus lentus subtilisin (Acc. No. 1GCI).
In a preferred embodiment, the 3D computerized model of one or more Plasmodium protease used according to the methods of the invention is a single homology model realized using at least two distinct Plasmodium subtilisin-like proteases (e.g. orthologs from Plasmodium vivax, Plasmodium falciparum and Plasmodium berghei).
In various embodiments, the methods of the invention permits to test candidate compounds against one or more Plasmodium subtilisin-like protease. Accordingly, the one or more Plasmodium subtilisin-like protease may be orthologous subtilisin-like proteases from different Plasmodium species (e.g. SUB1 from P. vivax then against SUB1 from P. falciparum and/or SUB1 from P. berghei). According to some embodiments, the in silico, in vitro, ex vivo and in vivo testing may be carried out on different strains of Plasmodium. In one particular embodiment the in silico docking step involves a 3D-model of a protease from Plasmodium vivax whereas in vitro and ex vivo testings involve a protease from Plasmodium vivax and/or Plasmodium falciparum, and in vivo testing involves an animal model for Plasmodium berghei infection. The one or more Plasmodium subtilisin-like protease may also consist of different enzymes, but from the same Plasmodium species (e.g. SUB1, SUB2 and/or SUB3 from P. vivax). Additional permutations are also possible (e.g. testing against (Pv)SUB1 and (Pf)SUB2).
Accordingly, in step (b) assessing in vitro inhibition of one or more Plasmodium subtilisin-like protease may comprise: (i) assessing in vitro inhibition of a subtilisin-like protease which is orthologous protease from a different species of Plasmodium than the Plasmodium subtilisin-like protease of step (a); and/or (ii) assessing in vitro inhibition of a subtilisin-like protease which is from a same Plasmodium species but a distinct protease than the Plasmodium subtilisin-like protease of step (a). Similarly, step (b) itself may comprises multiple testing of candidate compounds against one or more Plasmodium subtilisin-like protease and may comprise: (i) assessing in vitro inhibition of orthologous subtilisin-like proteases from at least two different species of Plasmodium; and/or (ii) assessing in vitro inhibition of distinct subtilisin-like proteases from a same Plasmodium species. Various testing experiments may also be performed in parallel (e.g. testing against (Pv)SUB1 and (Pf)SUB2). The in vitro testing step can consist in one or more of in vitro assays as described above. Other routinely in vitro assays can also be performed.
A further aspect, the invention relates to a method for identifying inhibitors of Plasmodium falciparum, comprising: (i) a first screening step directed in identifying potential inhibitors of Plasmodium vivax, and (ii) testing subsequently in vitro, ex vivo and/or in vivo potential inhibitors from step (i) for inhibition against Plasmodium vivax, Plasmodium falciparum and/or Plasmodium berghei. The first screening step comprises a step that is carried out in silico, more preferably by in silico docking a 3D structure of potential inhibitors into a 3D model of a Plasmodium vivax protease.
In preferred embodiments the Plasmodium vivax protease is a recombinant SUB1 protease, for instance a recombinant SUB1 protease comprising the amino acid sequence of PvSUB1-Bellem as defined at
In a particular embodiment of the screening methods described hereinbefore, candidate compounds are tested in silico (step (a)) using a 3D computerized model of SUB1 from P. vivax; next candidate compounds are tested in vitro (at step (b)) using SUB1 from P. vivax; next candidate compounds are tested ex vivo (step (c)) against P. falciparum; and then candidate compounds are tested in vivo (step (d)) against P. berghei.
In an another embodiment of the screening method described hereinbefore, candidate compounds are tested in silico (step (a)) using a 3D computerized model of SUB1 from P. falciparum; next candidate compounds are tested in vitro (at step (b)) using SUB1 from P. falciparum; next candidate compounds are tested ex vivo (step (c)) against P. falciparum; and then candidate compounds are tested in vivo (step (d)) against P. berghei.
The in vitro testing step can be performed using different types of assays, for instance by measuring the enzymatic activity of a Plasmodium subtilisin-like protease in presence of a compound to be tested. In a preferred embodiment, the assay is an enzymatic assay as described hereinbefore based on the cleavage of FRET (Fluorescent Resonance Energy Transfer) SUB-specific substrates. Suitable examples of substrates for SUB1 enzymes include, but are not limited to, those shown in Table 3. For performing an enzymatic assay, the Plasmodium protease may be produced and purified under a soluble active recombinant protein, or it may be purified from parasite-RBC culture by HPLC fractionation.
Inhibitory activity of the candidate compound may also be quantified. For instance, the in vitro testing may comprise: (i) measuring an inhibition constant (Ki) for the one or more Plasmodium subtilisin-like protease in presence of the candidate compound and/or (ii) measuring a half maximal inhibitory concentration (IC50) of the candidate compound on the one or more Plasmodium subtilisin-like protease. For instance, compounds having a Ki lower than about 50 μM, lower than 25 μM, lower than 10 μm or lower than 5 μM may be considered as interesting candidates for further testing and development.
The inhibition of the enzymatic activity of a Plasmodium subtilisin-like protease by a test compound could also be validated by quantification of the processed parasite target proteins using specific antibodies. Some of the natural substrates of SUB2 and SUB1 are known: AMA1 and MSP1-42 for SUB2, and SERA for SUB1. The effect of SUB1 inhibitors on SERA maturation can be evaluated for example, and is further illustrated in Examples.
Similarly, assessment of ex vivo efficacy of a test compound can be evaluated by measuring the EC50 (or IC50) constant for the test compound. Typically, the parasite culture is a Plasmodium falciparum or a Plasmodium vivax culture. Ex vivo cultivated Plasmodium can be chosen among references clones or among Plasmodium field isolates. A representative panel of P. falciparum and P. vivax parasites can be used for this type of assay.
The ex vivo testing step can consist in assessing the effect of a test compound on a Plasmodium stage-specific ex vivo culture. The ex vivo culture is for example composed of segmented schizonts of P. falciparum at 0.5% parasitemia and 1% hematocrit. The progress of the parasitemia from segmented schizonts to newly formed trophozoits, and the effect of test compound on this process, may be assessed by flow cytometry analysis.
The in vivo testing step can consist in measuring the effect of a test compound on red blood cell infection in Plasmodium-infected animals. The preferred parasited animal model is Plasmodium berghei-infected mice.
Kits
A further aspect of the invention relates to kits. The kits of the invention may be useful for the practice of the methods of the invention, particularly for in vitro screening of Plasmodium inhibitors.
A kit of the invention may comprise a tagged peptidic substrate as described herein and a protease, particularly a Plasmodium subtilisin-like protease. Preferably the protease comprises SEQ ID NO:4, and more preferably the protease is a recombinant protease. The kit may also comprise one or more additional components, such as incubation and assay buffer(s), controls, additional substrate(s), standards, detection materials (e.g. antibodies, fluorescein-labelled derivatives, luminogenic substrates, detection solutions, scintillation counting fluid, etc.), laboratory supplies (e.g. desalting column, reaction tubes or microplates (e.g. 96- or 384-well plates), a user manual or instructions, etc. Preferably, the kit and methods of the invention are configured such as to permit a quantitative detection or measurement of the protease activity.
Polynucleotides, Polypeptides and Cells
An addition aspect of the invention concerns nucleic and amino acid sequences as shown in
The invention further encompasses cells comprising a isolated polynucleotide as set forth in SEQ ID NO:1, SEQ ID NO:5 and/or SEQ ID NO:7, and cells comprising and/or expressing a polypeptide comprising SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6 and/or SEQ ID NO:8. Examples of cells encompassed by the invention include eukaryotic cells and more particularly cells suitable for baculovirus/insect cells expression system including, but not limited to, such as _sf9 and Hi5 cells.
II. Therapeutics
As exemplified hereinafter the methods of the invention successfully resulted in the identification of compounds having anti-malarial activity, in vitro, ex vivo and in vivo. In the context of the present invention, anti-malaria compounds, Plasmodium-inhibiting compounds, inhibitors of Plasmodium and anti-malaria candidates are equivalent terms (have the same meaning).
Accordingly, another aspect of the invention concerns anti-malaria compounds, and more particularly compounds inhibiting a Plasmodium protease. These compounds may be advantageously identified by the screening method of the invention. Preferably the Plasmodium protease is a subtilisin-like protease. In various embodiments the subtilisin-like protease is SUB1, SUB2 or SUB3.
The invention is also directed to methods for preventing, treating, improving, and/or alleviating a Plasmodium infection in a subject. The method comprises administering to the subject a therapeutically effective amount of a compound or of a pharmaceutical composition as defined herein. In some embodiments, a compound of the invention prevents, reduces and/or inhibits the Plasmodium parasite egress from and/or invasion into host cells. A related aspect concerns pharmaceutical compositions comprising a compound as defined herein. In preferred embodiments, the pharmaceutical composition is formulated as an anti-malarial drug (e.g. prophylaxis and/or treatment of malarial infections, including Plasmodium vivax and/or by Plasmodium falciparum infections). According to some embodiments, the compound of the invention is selected from the compounds in Table 1A. According to some embodiments, the compound of the invention is selected from the compounds in Table 1B:
The invention encompasses pharmaceutically acceptable salt of the compounds of the invention, including acid addition salts, and base addition salts. As used herein, the term “pharmaceutically acceptable salt” is intended to mean those salts which retain the biological effectiveness and properties of the free acids or bases, which are not biologically or otherwise undesirable. Desirable are salts of a compound are those salts that retain or improve the biological effectiveness and properties of the free acids and bases of the parent compound as defined herein or that takes advantage of an intrinsically basic, acidic or charged functionality on the molecule and that is not biologically or otherwise undesirable. Examples of pharmaceutically acceptable salts are also described, for instance, in Berge et al., “Pharmaceutical Salts”, J. Pharm. Sci. 66, 1-19 (1977).
The compounds of the present invention, or their pharmaceutically acceptable salts may contain one or more asymmetric centers, chiral axes and chiral planes and may thus give rise to enantiomers, diastereomers, and other stereoisomeric forms and may be defined in terms of absolute stereochemistry, such as (R)— or (S)— or, as (D)- or (L)- for amino acids. The present invention is intended to include all such possible isomers, as well as, their racemic and optically pure forms. Certain compounds of the present invention may exist in Zwitterionic form and the present invention includes Zwitterionic forms of these compounds and mixtures thereof.
In general, all compounds of the present invention may be prepared by any conventional methods, using readily available and/or conventionally preparable starting materials, reagents and conventional synthesis procedures.
The invention also encompasses the uses of a compound of the invention as defined herein, in combination with one or more existing anti-malarial drug (see hereinafter).
According to some embodiments, the compounds and compositions of the invention are capable of targeting more than one enzyme, presumably at different parasite stages, thereby maximizing efficacy, and/or minimizing risks of failure or resistance. Preferably, the compounds inhibit the activity of at least one subtilisin-like protease, more preferably, SUB1, SUB2 and/or SUB3.
According to some embodiments, the compounds and compositions of the invention are capable of inhibiting Plasmodium resistant strains, including but not limited to strains resistant to chloroquin, strains resistant to artemisinin, and/or strains resistant to derivatives of such anti-malarial drugs.
In preferred embodiments the compounds of the invention have Ki less than about 50 μM on recombinant subtilisin-like protease, and in more preferred embodiments less than 10 μM. In other preferred embodiments the compounds of the invention have an IC50 of about 20 μM or less, of about 1 μM or less, or about 100 nM or less. In some embodiments the compounds of the invention have an in vivo LD50 (in humans or animals) of about 33 mg/kg or less (e.g. ≦30 mg/kg, ≦10 mg/kg, or ≦1 mg/kg).
In a related aspect, the invention concerns a method for preventing, treating, improving, and/or alleviating a Plasmodium infection in a subject, the method comprising administering to the subject a therapeutically effective amount of a compound or of a pharmaceutical composition as defined herein.
The term “subject” includes living organisms in which a Plasmodium infection can occur. The term “subject” includes animals (e.g., mammals, e.g., cats, dogs, horses, pigs, cows, goats, sheep, rodents, e.g., mice or rats, rabbits, squirrels, bears, primates (e.g., chimpanzees, monkeys, gorillas, and humans)), as well as wild and domestic bird species (e.g. chickens), and transgenic species thereof. Preferably, the subject is a mammal. More preferably, the subject is a human.
The pharmaceutical compositions of the invention may comprise a therapeutic agent (e.g. a compound listed in Table 1A or 1B or a compound identified by the above screening method) in a pharmaceutically acceptable excipient, carrier, buffer, stabilizer or other materials well known to those skilled in the art. Such materials should be non-toxic and should not interfere with the efficacy of the active ingredient. The precise nature of the carrier or other material may depend on the route of administration, e.g. oral, intravenous, cutaneous or subcutaneous, nasal, intramuscular, and intraperitoneal routes.
The pharmaceutical compositions of the invention may comprise a compound of the invention as defined herein, in combination with one or more existing anti-malarial drug, including but not limited to chloroquine FNA, resochin, dawaquin, artemisinin, quinine, amodiaquine, sulfadoxynie, pyrimethamine, mefloquine, proguanil, artesunate, halofantrine, and atovaquone.
With respect to pharmaceutically useful compounds or compositions according to the present invention that is to be given to an individual, administration is preferably in a “prophylactically effective amount” or a “therapeutically effective amount” (as the case may be, although prophylaxis may be considered therapy), this being sufficient to show benefits to the individual.
Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, numerous equivalents to the specific procedures, embodiments, claims, and examples described herein. Such equivalents are considered to be within the scope of this invention and covered by the claims appended hereto. The invention is further illustrated by the following examples, which should not be construed as further limiting.
Red blood cell egress and invasion by Plasmodium parasites strictly depend upon the precise maturations of parasite proteins SERA5, a cystein protease implicated in the rupture of the parasitophorous vacuole membrane and MSP1 (Merozoite Surface Protein 1). The parasite subtilisin-like serine protease SUB1 plays a key role in the process (S. Yeoh et al, Cell, 131(6), 1072-83 (2007)) as it is essential for the merozoite egress. On the other hand, SUB2, another subtilisin-like serine protease is essential for the merozoite entry into RBC. Taking advantage of the similarity of SUB1 active site with bacterial subtilisins, we have used an in silico screening approach and have identified inhibitors of Plasmodium.
A general strategy for screening and validation of Plasmodium inhibitors according to a preferred embodiment of the invention is summarized in
The in silico step was based on in silico docking of test compounds into SUB1 modeled active sites, and more particularly a 3D model of a recombinant SUB1 protein (PvSUB1) derived from Plasmodium vivax sequences.
The selection and optimization of the PvSUB1 optimized model is illustrated in
It is the amino acid sequence of PvSUB1 of Plasmodium vivax Bellem isolate which was used for creating the PvSUB1 optimized model described hereinabove (see
The PvSUB1, PfSUB1 and PbSUB1 recombinant purified enzymes expressed using the baculovirus/insect cells expression system, in combination with a FRET assay, were used for Ki determination. The nucleotide and the amino acid sequences of each of PvSUB1, PfSUB1 and PbSUB1 are shown in
Briefly, SUB1 proteins exist under a pro-form (80 kDa) and an active form (48-50 kDa).
HPLC-fractions of purified recombinant PvSUB1 were tested for enzymatic activity using the FRET-specific based assay. For each HPLC-fractions, the enzymatic initial velocity (V, expressed in Arbitrary Fluorescence Unit/minutes) has been determined, showing that PvSUB1 active enzyme accumulates mostly in fractions B7 and B8 (
P. falciparum
Next, the selected SUB1 inhibitors were evaluated biologically for their impact on P. falciparum 3D7 stage-specific ex vivo culture.
Finally, the compounds were tested in vivo on P. berghei-infected mice. The compounds inhibited red blood cell infection in a dose-dependent manner. It was estimated that the compounds has a LD50 of about 33 mg/kg (LD50 of chloroquine is about 2 mg/kg) without showing any obvious signs of toxicity.
Altogether these results demonstrate that targeting a Plasmodium vivax therapeutic target leads to the selection and the validation of chemical compounds having a potent activity against different Plasmodium species, which are responsible for the severe forms of malaria. Therefore the screening methods and the chemical compounds described herein are potentially useful in anti-malaria therapy and prophylaxis against at least the two main Plasmodium infecting humans: P. vivax and P. falciparum.
The homology modeling procedure was realized using the suite of tools, Biskit. In many ways, Biskit presents features to produce models as accurate as possible (Grünberg R, et al., A software platform for structural bioinformatics, Bioinformatics. 2007, 23(6):769-70). The multiple alignments and the construction of models are the most critical task of modeling. Biskit use respectively 3DCoffee™ (O'Sullivan et al. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol. 2004, 340(2):385-95) and Modeller™ (Sall and Blundell. Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 1993, 234(3): 779-815). For this study, modeling of PvSUB1 enzyme is restricted to its catalytic domain from residue 1302 to P586, which present a significant homology to bacterial subtilisins. Proteins structures displaying significant sequence similarities with PvSUB1 were searched in the PDB (Protein Data Bank) database using Blast (Altschul et al. Basic local alignment search tool. J Mol Biol. 1990, 215(3):403-10). Several homologous proteins have been identified and only proteins with an e-value less than 0.001 and a resolution inferior to 2.5 A were considered. Then, structures were clustered according to their sequence similarities using Blastclust with the parameters simcut 1.75 and simlen 0.9 thereby doing 7 clusters. We decided to keep as template the structure of best resolution in each cluster, selecting in this way 7 templates, presented in the Table 5. The sequence identities of the catalytic domain of these templates with PvSUB1 and PfSUB1's are shown in Table 6.
Bacillus
amyloliquifaciens
Bacillus Sphaericus
Thermoactinomyces
vulgaris
Bacillus sp.
Bacillus licheniformis
Tritirachium album
Bacillus lentus
Bacillus lentus
To be meaningful and reliable, a multiple sequence requires a large number of aligned sequences. Thus, protein sequences were also searched in the non-redundant sequence database of the Swiss-Prot Protein Knowledgebase (Boeckmann B. et al., The Swiss-Prot Protein Knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:365-370 (2003); www.ncbi.nlm.nih.gov) displaying significant with an e value <0.01. 73 sequences clustered according to their similarities into 50 clusters, from each of which the member of longest sequence was further considered. The multiple sequence alignment of the target sequence in addition to the 7 template sequences and the additional 50 homologous sequences (Table 7) was performed using 3DCoffee™ which rely on structural alignments and local sequence alignment in order of producing a global alignment of all sequences (O'Sullivan, 2004, supra; Dalton and Jackson. An evaluation of automated homology modelling methods at low target template sequence similarity. Bioinformatics 2007, 23(15): 1901-8). Modeller™ version 7v7 was used to construct 50 3D-models of PvSUB1, guided from the sequences alignment and the 7 templates structures.
Selection and Validation of the 3D Models
The quality of the 3D-models was verified with ProCheck™ PROCHECK and Prosa II™ (Laskowski et al. PROCHECK: a program to check the stereochemical quality of protein structures. J of Applied Crystallography 1993, 26(2): 283-291). The structures analyzed by the ProCheck™ program present only few residues in disabled region of the Ramachandran diagram. These residues are situated in large inserted loops which mainly correspond to insertions into the PvSUB1 or PfSUB1 sequences compared to the templates, which can explain some deviation with respect to statistically observed geometries in experimental structures.
The ab initio construction by Modeller™ of these regions does not guaranty a reliable geometry. Nevertheless, such imprecision does not alter the correct construction of the binding site.
The active site was almost identical in all models, as expected from the very small deviation observed in the corresponding region of the template structures. The global root mean square deviation (RMSD) on all main chain atoms observed between the models was close to 2 Å. However, as could be anticipated, the main differences were found in the topology of the large inserts situated at the surface of the protein, far from the active site. The RMSD between all models calculated on all atoms of the active site pocket was equal to 0.1 Å. In other words, they were basically equivalent in this region, and the level of confidence in the conformation of the modeled active site was high, which allowed choosing one of the models for the following studies.
A suitable characterization of the residues composing the binding pocket is a prerequisite to restrict the docking to a relevant area of the catalytic site. Competitive inhibitors should bind and interact with these selected residues.
The binding pocket was selected by superimposition of the PvSUB1 model to one of its template, the crystallographic structure of thermitase bound to the subtilisin inhibitor Eglin (2TEC) (Gros et al., Molecular dynamics refinement of a thermitase-eglin-c complex at 1.98 A resolution and comparison of two crystal forms that differ in calcium content. J Mol Biol. 1989, 210(2): 347-67). Binding site was defined by the residues of PvSUB1 model which have at least one atom up to 6 Å from the Eglin pentapeptide P1′-P5. This region corresponds to the burriest part of the active site, which is as described by Siezen & Leunissen (Siezen and Leunissen. Subtilases: the superfamily of subtilisin-like serine proteases. Protein Sci. 1997, 6(3): 501-23.) primary for the substrate recognition. Moreover the Icm Pocket-Finder algorithm based on the exploration of the whole enzyme surface predicts/detects this same region as the most “druggable” pocket. Thus, the active site used for all docking experiments was composed of the entire residues D316, S317, N370, Y371, H372, L405, D406, H408, L410, G411, M416, S434, F435, S436, S461, A462, S463, N464, C465, P473, Y486, P488, Y511, L545, N546, G547, T548, S549 and M550. Consistent with the first step of the catalytic mechanism, the side chain of residue H372 that belongs to the catalytic triad was described in its uncharged form, i.e. with a single proton born by the Nd nitrogen atoms of the indole ring.
Set Up of the Chemical Database
The virtual screening was performed using the commercially available compounds from Chemdiv, Inc (chemdiv.com). The Chemdiv molecules were filtered using the program Filter (openeye.com), with standard parameters to select “drug-like” compounds. Predicted aggregators and toxic compounds were also eliminated. The 149 992 remaining compounds were converted as 3D conformers corresponding to a structure of minimized energy was generated with Corina (molecular-networks.com) and considered as an entry for the screening described above.
Virtual Screening
We used two of the most performing docking programs Icm (Totrov and Abagyan. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins 1997, Suppl 1: 215-20) and FlexX™ (Rarey et al., A fast flexible docking method using an incremental construction algorithm. J Mol Biol. 1996, 261(3): 470-89), to extract relevant in silico hits from the selected 149 992 drug-like compounds. Icm was applied with its standard parameters. In parallel, we used FlexX to select a second pool of compounds. Unlike Icm, which requires 30 s to 1 minute to dock one compound, FlexX™ is faster, allowing to process different screening conditions. Thus FlexX™ was run using 3 different 3D-models of PvSUB1 selected from the 50 generated by Modeller™.
Screening was also performed, under pharmacophore restraints (Hindle, 2002). In many cases, the resolved subtilisins 3D-structures available in the PDB correspond to a complex composed of the enzyme catalytic domain co-crystallised with an inhibitor. We focused on 1 LW6, 1 R0R, 2TEC and on 1 BH6: the analyses of these four structures show that five inter-molecular hydrogen bonds are conserved and are involved in the interactions between conserved subtilisins residues and their ligands.
Therefore, we postulated that a screening protocol selecting molecules able to bind PvSUB1 using these conserved hydrogen bonds would help identifying better competitive inhibitors. However, a preliminary test using these four hydrogen bonds as a pharmacophore restraint was shown to be too drastic to find any docking solution. Therefore, we used FlexX™ to select molecules predicted to interact with the PvSUB1 3D-models with two of these four conserved hydrogen bonds.
PfSUB1 and PvSUB1 Production
Recombinant baculoviruses expressing recombinant forms of PvSUB1 and PfSUB1 were amplified by infecting 5×106 Sf9 cells in T-25 culture cultivated in Insect XPRESS medium (Lonza) supplemented with 5% fetal calf serum and 50 mg/L gentamycin. The final viral stock was titrated by end-point dilution assay. For large-scale protein production, Sf9 cells (1 L at 3×106 cells/mL) were infected for 72 h with recombinant baculovirus at a MOI of 10 in Insect Xpress™ medium supplemented with 50 mg/L gentamycin and 0.5 μg/mL of tunicamycine.
PfSUB1 and PvSUB1 Purification
PvSUB1 and PfSUB1 Culture supernatant containing the secreted and active PvSUB1 or PfSUB1 recombinant enzymes was harvested, centrifuged 30 min at 2150 rcf to remove cells and cellular debris and concentrated/diafiltrated against D-PBS 0.5 M NaCl; 5 mM Imidazole (loading buffer). The protein was purified on an AKTA™ purifier system (GE Healthcare). The sample was loaded onto a 3 mL TALON™ Metal affinity resin (Clontech Laboratories) previously equilibrated in loading buffer, thus allowing the binding of PvSUB1 or PfSUB1 recombinant proteins via the addition of a 6×-histidines tag in its C-terminal. The column was extensively washed with loading buffer and the bound protein was eluted with a linear gradient from 5 to 200 mM imidazole in D-PBS 0.5 M NaCl. Fractions containing PvSUB1 or PfSUB1 were pooled concentrated using a Amicon Ultra 15™ (10000 MWCO) and size fractionated onto a HiLoad™ 16/60 Superdex™ 75 column equilibrated with 20 mM Tris pH 7.5, 100 mM NaCl to remove imidazole and exchange buffer. Throughout the purification procedure, fractions were monitored by absorbance (280 nm) and analyzed by Coomassie blue staining of SDS-PAGE gels and activity assay. Fractions containing the PvSUB1 or PfSUB1 purified proteins were pooled, and protein concentration was determined using the BCA Protein Assay following manufacturer's recommendations (Bio Basic). Purified PvSUB1 or PfSUB1 recombinant proteins were stored at −20° C. following the addition of 30% v/v of pure glycerol.
PfSUB1 and PvSUB1 Enzymatic Assays
For the kinetic assays we used the recombinant PvSUB1/PfSUB1 enzymes and specific peptide substrates whose sequence are deduced from the auto-maturation site of each one: KLVGADDVSLA (SEQ ID NO: 9), which cleavage occurs between the two aspartates for PvSUB1 and KLVSADNIDIS (SEQ ID NO: 11) which is cleaved between the aspartate and the asparagine for PfSUB1. The substrates used had the fluorophores/quencher Dabsyl/Edans or DYQ660/DY630 at each edge. The enzymatic assays were performed with 13 ng of purified PvSUB1 or PfSUB1 in 20 mM Tris pH 7.5 and 25 mM CaCl2 at 37° C. The apparent Km of PfSUB1 and PvSUB1 for their substrate being 30.2 μM±3.4 and 19.7 μM±1.7 respectively, all further experiments were performed using 25 μM of substrates. For the determination of the Ki, the compounds, previously resuspended in 100% DMSO at 10 mM, were tested at ten different concentrations ranging from 300 μM to 585 nM following sequential 1:2 dilutions. The final mixture was distributed in duplicate into a 384-well black microtiter plate (Thermo Scientific) and the fluorescence was monitored every 3 minutes for 90 min at 37° C. in a Labsystems Fluoroskan Ascent™ spectrofluorometer or a Tecan Infinite M1000™ spectrofluorometer using the excitation and emission wavelengths of 460/500 nm or 620/680 nm for the Dabsyl/Edans or DYQ660/DY630 substrates respectively. The slope of the linear part of the kinetic was determined in an Excel™ (Microsoft) spreadsheet. Every steps of the enzymatic assay were done on ice to make sure that the protein was not active before the measure of the fluorescence. The Ki and IC50 values were determined (N=3) using GraphPad Prism™ software.
The enzymatic assay using approximately 13 ng of purified PvSUBI, in 20 mM Tris pH 7.5 and 25 mM CaCl2 at 37° C. in presence of 25 μM the Dabsyl-KLVGADDVSLA-Edans (Dabsvl-SEQ ID NO: 9-EDANS) has been validated on 384-well plates and is suitable for High Throughput Screening (HTS) with an average Z−0.52±0.04 [Zhang et al 1999, J Biomol Screen 4(2):67-73].
Culture Tests
Parasite Culture and In Vitro Drug Susceptibility Assay
Asexual cultures of reference clone 3D7 obtained from MR4 (MR4.org) was maintained in continuous cultures following the method of Trager and Jensen [1976, Science 193: 673-5], except that the medium was composed of RPMI 1640 medium supplemented with 10% decomplemented human serum (AB+), hypoxanthine 100 μM, gentamycin 50 ng/ml_. Parasites were incubated at 37° C. in an atmosphere composed of 5% O2, 5% CO2 and 90% N2. Quantitative assessment of the antimalarial activity of test compound was performed as described by Desjardins et al[1979, Antimicrob Agents Chemother 16:710-8.] and Bougdour et al[2009, J Exp Med 206: 953-66] on asynchronous culture of clone 3D7 (0.5% parasitemia and 1% hematocrit), except that the parasites were in contact with the drug for 48 hours, the culture medium contained 10 μM hypoxanthine. IC50/EC50 have been determined following nonlinear regression analysis using HN-NonLin V1.1 software (malaria.farch.net).
Flow Cytometry Analysis
A synchronised culture composed of segmented schizonts of P. falciparum (3D7 clone) at 0.5% parasitemia and 1% hematocrit is performed in a 24 wells plate. An aliquot corresponding to 10% of the starting culture (T0) is diluted in a solution at 0.04% of glutaraldehyde in PBS (Dulbecco) and store at 4° C. for further flow cytometry analysis. E64, a cysteine-protease inhibitor known to block the egress of P. falciparum merozoites in vitro [Salmon et al. 2001 Proc Natl Acad Sci USA 98: 271-6.] was used as a positive control at a final concentration of 10 μM, while the compounds were tested at a final concentration of 90 μM and a mock control (DMSO) received 0.9% DMSO, in which compounds are resuspended. The final experiment ended after an incubation of 12 hours, allowing the rupture of the parasitized erythrocytes, the egress of merozoites and their subsequent entry into fresh red blood cells. 10% of the cultures are resuspended in a solution of 0.04% glutaraldehyde in PBS (Dulbecco) and store at 4° C. for flow cytometry analysis. The progress of the parasitaemia from segmented schizont to newly formed trophozoites was assessed by flow cytometry after staining samples by the DNA-binding fluorescent dye, YOYO-1™, as previously described by Li and colleagues [2007, Cytometry A 71: 297-307.] with some modifications. Briefly, following a centrifugation at 450 g for 5 min the pelleted cells were re-suspended in 0.3 ml PBS (Dulbecco) supplemented with 0.25% Triton X-100™ and incubated for 10 min at room temperature. After centrifugation, the permeabilized cells were re-suspended in 500 μL of RNase at 50 μg/mL and incubated for at least 3 h at 37° C. Then YOYO-1™ solution (Invitrogen) was added to obtain a final concentration of 500 ng/mL. Samples were incubated at 4° C. in darkness for at least 4 h and centrifuged at 450 g for 5 min. The pelleted cells were re-suspended in 0.3 ml PBS before being analysed by flow cytometry using a FACSCanto™ (BD) apparatus and the data were analyzed using FlowJo™ (Tree Star) software. The fluorescent signal of YOYO-1™ dying cells was collected in FL-1 channel after compensation of fluorescent intensity in the FL-2 channel.
Headings are included herein for reference and to aid in locating certain sections These headings are not intended to limit the scope of the concepts described therein under, and these concepts may have applicability in other sections throughout the entire specification Thus, the present invention is not intended to be limited to the embodiments shown herein but is to be accorded the widest scope consistent with the principles and novel features disclosed herein.
As used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural referents unless the context clearly indicates otherwise. Thus, for example, reference to “a compound” includes one or more of such compounds, and reference to “the method” includes reference to equivalent steps and methods known to those of ordinary skill in the art that could be modified or substituted for the methods described herein.
Unless indicated to the contrary, the numerical parameters set forth in the present specification and attached claims are approximations that may vary depending upon the properties sought to be obtained. Notwithstanding that the numerical ranges and parameters setting forth the broad scope of the embodiments are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. Any numerical value, however, inherently contain certain errors resulting from variations in experiments, testing measurements, statistical analyses and such.
It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the present invention and scope of the appended claims.
| Filing Document | Filing Date | Country | Kind | 371c Date |
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| PCT/IB2010/003423 | 11/29/2010 | WO | 00 | 1/6/2014 |
| Publishing Document | Publishing Date | Country | Kind |
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| WO2012/073066 | 6/7/2012 | WO | A |
| Number | Date | Country |
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| 2006120579 | Nov 2006 | WO |
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| Number | Date | Country | |
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| 20140134657 A1 | May 2014 | US |
