Differences in substrate specificities between cysteine protease CPB isoforms of Leishmania mexicana are mediated by a few amino acid changes

Flavonoid Derivatives as New Potent Inhibitors of Cysteine Proteases: An Important Step toward the Design of New Compounds for the Treatment of Leishmaniasis

Leishmaniasis is a neglected tropical disease, affecting more than 350 million people globally. However, there is currently no vaccine available against human leishmaniasis, and current treatment is hampered by high cost, side-effects, and painful administration routes. It has become a United Nations goal to end leishmaniasis epidemics by 2030, and multitarget drug strategy emerges as a promising alternative. Among the multitarget compounds, flavonoids are a renowned class of natural products, and a structurally diverse library can be prepared through organic synthesis, which can be tested for biological effectiveness. In this study, we synthesised 17 flavonoid analogues using a scalable, easy-to-reproduce, and inexpensive method. All synthesised compounds presented an impressive inhibition capacity against rCPB2.8, rCPB3, and rH84Y enzymes, which are highly expressed in the amastigote stage, the target form of the parasite. Compounds 3c, f12a, and f12b were found to be effective against all isoforms. Furthermore, their intermolecular interactions were also investigated through a molecular modelling study. These compounds were highly potent against the parasite and demonstrated low cytotoxic action against mammalian cells. These results are pioneering, representing an advance in the investigation of the mechanisms behind the antileishmanial action of flavonoid derivatives. Moreover, compounds have been shown to be promising leads for the design of other cysteine protease inhibitors for the treatment of leishmaniasis diseases.

Antileishmanial activity and insights into the mechanisms of action of symmetric Au(I) benzyl and aryl-N-heterocyclic carbenes

Leishmania amazonensis and L. braziliensis are the main etiological agents of the American Tegumentary Leishmaniasis (ATL). Taking into account the limited effectiveness and high toxicity of the current drug arsenal to treat ATL, novel options are urgently needed. Inspired by the fact that gold-based compounds are promising candidates for antileishmanial drugs, we studied the biological action of a systematic series of six (1)-(6) symmetric Au(I) benzyl and aryl-N-heterocyclic carbenes. All compounds were active at low micromolar concentrations with 50% effective concentrations ranging from 1.57 to 8.30 μM against Leishmania promastigotes. The mesityl derivative (3) proved to be the best candidate from this series, with a selectivity index ~13 against both species. The results suggest an effect of the steric and electronic parameters of the N-substituent in the activity. Intracellular infections were drastically reduced after 24h of (2)-(5) incubation in terms of infection rate and amastigote burden. Further investigations showed that our compounds induced significant parasites' morphological alterations and membrane permeability. Also, (3) and (6) were able to reduce the residual activity of three Leishmania recombinant cysteine proteases, known as possible targets for Au(I) complexes. Our promising results open the possibility of exploring gold complexes as leishmanicidal molecules to be further screened in in vivo models of infection.

Targeting of the Leishmania mexicana cysteine protease CPB2.8ΔCTE by decorated fused benzo[b]thiophene scaffold

A potent and highly selective anhydride-based inhibitor ofLeishmania mexicanacysteine protease CPB2.8 (IC₅₀= 3.7 μM) was investigated by inhibition assays, NMR biomimetic experiments and docking studies.

Natural products as inhibitors of recombinant cathepsin L of Leishmania mexicana

Cysteine proteinases (cathepsins) from Leishmania spp. are promising molecular targets against leishmaniasis. Leishmania mexicana cathepsin L is essential in the parasite life cycle and a pivotal in virulence factor in mammals. Natural products that have been shown to display antileishmanial activity were screened as part of our ongoing efforts to design inhibitors against the L. mexicana cathepsin L-like rCPB2.8. Among them, agathisflavone (1), tetrahydrorobustaflavone (2), 3-oxo-urs-12-en-28-oic acid (3), and quercetin (4) showed significant inhibitory activity on rCPB2.8 with IC50 values ranging from 0.43 to 18.03 µM. The mechanisms of inhibition for compounds 1-3, which showed Ki values in the low micromolar range (Ki = 0.14-1.26 µM), were determined. The biflavone 1 and the triterpene 3 are partially noncompetitive inhibitors, whereas biflavanone 2 is an uncompetitive inhibitor. The mechanism of action established for these leishmanicidal natural products provides a new outlook in the search for drugs against Leishmania.

Heparin modulates the endopeptidase activity of Leishmania mexicana cysteine protease cathepsin L-Like rCPB2.8

Background

Cysteine protease B is considered crucial for the survival and infectivity of the Leishmania in its human host. Several microorganism pathogens bind to the heparin-like glycosaminoglycans chains of proteoglycans at host-cell surface to promote their attachment and internalization. Here, we have investigated the influence of heparin upon Leishmania mexicana cysteine protease rCPB2.8 activity.

Methodology/Principal Findings

The data analysis revealed that the presence of heparin affects all steps of the enzyme reaction: (i) it decreases 3.5-fold the k₁ and 4.0-fold the k₋₁, (ii) it affects the acyl-enzyme accumulation with pronounced decrease in k₂ (2.7-fold), and also decrease in k₃ (3.5-fold). The large values of ΔG  =  12 kJ/mol for the association and dissociation steps indicate substantial structural strains linked to the formation/dissociation of the ES complex in the presence of heparin, which underscore a conformational change that prevents the diffusion of substrate in the rCPB2.8 active site. Binding to heparin also significantly decreases the α-helix content of the rCPB2.8 and perturbs the intrinsic fluorescence emission of the enzyme. The data strongly suggest that heparin is altering the ionization of catalytic (Cys²⁵)-S⁻/(His¹⁶³)-Im⁺ H ion pair of the rCPB2.8. Moreover, the interaction of heparin with the N-terminal pro-region of rCPB2.8 significantly decreased its inhibitory activity against the mature enzyme.

Conclusions/Significance

Taken together, depending on their concentration, heparin-like glycosaminoglycans can either stimulate or antagonize the activity of cysteine protease B enzymes during parasite infection, suggesting that this glycoconjugate can anchor parasite cysteine protease at host cell surface.

Foot and mouth disease leader protease (Lbpro): Investigation of prime side specificity allows the synthesis of a potent inhibitor

Foot and mouth disease virus expresses its genetic information as a single polyprotein that is translated from the single-stranded RNA genome. Proteinases contained within the polyprotein then generate the mature viral proteins. The leader protease (Lb(pro)) performs the initial cleavage by freeing itself from the growing polypeptide chain; subsequently, Lb(pro) cleaves the two homologues of the host cell protein eukaryotic initiation factor 4G (eIF4G). We showed that Lb(pro) possesses specific binding sites at the non prime side from S(1) down to S(7) [Santos et al. (2009) Biochemistry, 48, 7948-7958]. Here, we demonstrate that Lb(pro) has high prime side specificity at least down to the S'(5) site. Lb(pro) is thus not only one of the smallest papain-like cysteine peptidases but also one of the most specific. It can still however cleave between both K↓G and G↓R pairs. We further determined the two-step irreversible inhibition (E + I ↔ EI→ E - I) kinetic parameters of two known irreversible epoxide-based inhibitors of cysteine proteinases, E64 and CA074 on Lb(pro) that show for the reversible step (E + I ↔ EI) K(i) = 3.4 μM and 11.6 μM, and for the irreversible step (EI→E-I) k(4) = 0.16 and 0.06 min(-1), respectively. Knowledge of the Lb(pro) specificity led us to extend E64 by addition of the dipeptide R-P. This compound, termed E64-R-P-NH(2), irreversibly inhibited Lb(pro) with a K(i) = 30 nM and k(4) = 0.01 min(-1) and can serve as the basis for design of specific inhibitors of FMDV replication.

Cysteine proteases as potential antigens in antiparasitic DNA vaccines

Cysteine proteases in parasites are potent inducers of vertebrate host immune responses and may under certain circumstances take part in the pathogen's immune evasion strategies. These capacities place these parasite molecules as interesting candidate antigens in antiparasitic vaccines for use in vertebrates. Parasite cysteine proteases are able to skew the Th1/Th2 profile in mammals towards a response which allows sustainable parasite burdens in the host. DNA vaccines are also able to skew the Th1/Th2 profile by different administration techniques and the use of cysteine proteases in these genetic immunizations open perspectives for manipulation of the host immune response towards higher protection.

Characterization of alpha-isopropylmalate synthases containing different copy numbers of tandem repeats in Mycobacterium tuberculosis

BACKGROUND

Alpha-isopropylmalate synthase (alpha-IPMS) is the key enzyme that catalyzes the first committed step in the leucine biosynthetic pathway. The gene encoding alpha-IPMS in Mycobacterium tuberculosis, leuA, is polymorphic due to the insertion of 57-bp repeat units referred to as Variable Number of Tandem Repeats (VNTR). The role of the VNTR found within the M. tuberculosis genome is unclear. To investigate the role of the VNTR in leuA, we compared two alpha-IPMS proteins with different numbers of amino acid repeats, one with two copies and the other with 14 copies. We have cloned leuA with 14 copies of the repeat units into the pET15b expression vector with a His6-tag at the N-terminus, as was previously done for the leuA gene with two copies of the repeat units.

RESULTS

The recombinant His6-alpha-IPMS proteins with two and 14 copies (alpha-IPMS-2CR and alpha-IPMS-14CR, respectively) of the repeat units were purified by immobilized metal ion affinity chromatography and gel filtration. Both enzymes were found to be dimers by gel filtration. Both enzymes work well at pH values of 7-8.5 and temperatures of 37-42 degrees C. However, alpha-IPMS-14CR tolerates pH values and temperatures outside of this range better than alpha-IPMS-2CR does. alpha-IPMS-14CR has higher affinity than alpha-IPMS-2CR for the two substrates, alpha-ketoisovalerate and acetyl CoA. Furthermore, alpha-IPMS-2CR was feedback inhibited by the end product l-leucine, whereas alpha-IPMS-14CR was not.

CONCLUSION

The differences in the kinetic properties and the l-leucine feedback inhibition between the two M. tuberculosis alpha-IPMS proteins containing low and high numbers of VNTR indicate that a large VNTR insertion affects protein structure and function. Demonstration of l-leucine binding to alpha-IPMS-14CR would confirm whether or not alpha-IPMS-14CR responds to end-product feedback inhibition.

Expression and substrate specificity of a recombinant cysteine proteinase B of Leishmania braziliensis

The cysteine proteinase B of Leishmania parasites is an important virulence factor. In this study we have expressed, isolated and characterized for the first time a recombinant CPB from Leishmania braziliensis, the causative agent of mucocutaneous leishmaniosis. The mature region of the recombinant CPB shares a high percentage identity with its Leishmania mexicana CPB2.8 (rCPB2.8DeltaCTE) counterpart (76.36%) and has identical amino acid residues at the S(1), catalytic triad and S'(1) subsites. Nevertheless, when the kinetics of substrate hydrolysis was measured using a combinatorial library of internally quenched fluorescent peptides based upon the lead sequence Abz-KLRSSKQ-EDDnp, significant differences were obtained. These results suggest that the differences in substrate utilization observed between the L. mexicana and L. braziliensis CPs must be related to amino acid modifications outside the core of the active site cleft. Moreover, a potent inhibitor with Pro at P1 and high affinity for L. braziliensis recombinant CPB showed less affinity to L. mexicana CPB 2.8, which preferred Phe, Leu, and Asn at the same position.

Trypanoplasma borreli cysteine proteinase activities support a conservation of function with respect to digestion of host proteins in common carp

Trypanoplasma borreli is an extracellular parasite that is transmitted by a leech vector and is naturally found in the blood of cyprinid fish. High parasitemia and associated severe anemia together with splenomegaly are typical of infection of common carp, Cyprinus carpio L. Papain-like cysteine proteinases expressed by trypanosome parasites contribute to the pathogenicity of trypanosomes, and are considered an important target for the development of new trypanocidal drugs. T. borreli is a member of the Parabodonida, sharing a common ancestor with the other Kinetoplastida. We demonstrate the presence of a cysteine proteinase expressed by T. borreli. Alignment of the sequence with other kinetoplastid cysteine proteinase sequences supports the phylogenetic hypotheses based on analyses of ribosomal RNA genes. We expressed the T. borreli cysteine proteinase in Escherichia coli, refolded the purified protein into a biologically active proteinase and showed it has cathepsin L-like activity. Addition of the (non)active proteinase to in vitro-derived carp head kidney-derived macrophages did not significantly modulate macrophage activity. Immunization of carp with the recombinant proteinase did induce a very high increase in proteinase-specific antibodies but only slightly lowered parasitemia. Digestion of host hemoglobin and immunoglobulin by the cysteine proteinase likely contribute to the pathogenicity of T. borreli. The possibility that digestion by the cysteine proteinase of host transferrin could contribute to an innate activation profile of macrophages in vivo is discussed. Our findings suggest a conservation of function with respect to cysteine proteinase activity in the Parabodonida in support of the hypotheses on the phylogeny of the Kinetoplastida.

Specific cpb copies within the Leishmania donovani complex: evolutionary interpretations and potential clinical implications in humans

Leishmania infantum and Leishmania donovani both pertain to the L. (L.) donovani complex and are responsible for visceral leishmaniasis. To explore the L. donovani complex, we focused our study on cysteine protease B (cpb) and especially on 2 cpb copies: cpbE and cpbF. We selected cpb genes because of their phylogenetic interest and host-parasite interaction involvement. Sequencing these 2 copies revealed (i) that cpbE is specific to L. infantum and cpbF is specific to L. donovani and (ii) that these 2 copies are different in length and sequence. Phylogenetic analysis and protein predictions were carried out in order to compare these copies (i) with other trypanosomatid cpb, especially L. mexicana, and (ii) within the L. donovani complex. Our results revealed patterns specific to the L. donovani complex such as the COOH-terminal extension, potential epitopes and N-glycosylation sites. Moreover, phylogenetic analysis revealed different levels of polymorphism between L. infantum and L. donovani and confirmed the ancestral status of the latter. L. infantum has a shorter sequence and a deleted sequence responsible for modifications in protein conformation and catalytic triad. Considering the clinical aspect, L. infantum dermotropic strains appeared more polymorphic than L. infantum viscerotropic strains.

Specific negative charges in cysteine protease isoforms of Leishmaniamexicana are highly influential on the substrate binding and hydrolysis

We focused on the importance of the electrostatic environment on the catalytic properties of the Leishmania mexicana CPB recombinant isoenzymes (rCPB2.8, rCPB3 and its mutant rH84Y), by investigating the influence of pH and NaCl on their hydrolytic activities. rCPB2.8 contains the residues Asn60, Asp61 and Asp64; rCPB3 presents the three variant residues Asp60, Asn61 and Ser64 and the mutant of the latter isoform, rH84Y, has a mutation on the outer loop residue (His84 to Tyr). Synthetic fluorescence resonance energy transfer (FRET) peptides, which contain different positive charge distribution in their sequences were used as substrates. The results show that hydrolytic efficiency is dependent of the positive charge distribution in the substrates and that NaCl activated rCPB2.8 and rCPB3 in acidic pH but inhibited them at pH higher than 5. The rate constants of substrate diffusion (k1), substrate dissociation (k-1), acylation (k2) and deacylation (k3) and the corresponding activation energies and entropies were derived. Significant differences in the kinetic rate constants (k) and entropies were found between the CPB isoforms, and the diffusion process seems to be the limiting step. The activation energy of denaturation (Ea-Den) and entropy of denaturation (DeltaSDen) of rCPB3 were higher than those for rCPB2.8, suggesting higher salvation and protein structure for rCPB3. Thus the findings suggest that the two CPB isoenzymes with a few negative charge modifications provide the parasite with an array of hydrolytic activity and enzymatic adaptation to pH, salinity and temperature that may be needed for its interaction with the mammalian host.