Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum

Published in: Nature Communications, Volume: 14, Issue: 1, Pages: 3059

DOI: 10.1038/s41467-023-38774-1

Authors: Kumpornsin, Krittikorn; Kochakarn, Theerarat; Yeo, Tomas ; Okombo, John ; Luth, Madeline R.; Hoshizaki, Johanna ; Rawat, Mukul; Pearson, Richard D. ; Schindler, Kyra A. ; Mok, Sachel ; Park, Heekuk ; Uhlemann, Anne-Catrin ; Jana, Gouranga P. (TCGLS Member); Maity, Bikash C. (TCGLS Member); Laleu, Benoit ; Chenu, Elodie; Duffy, James; Moliner Cubel, Sonia; Franco, Virginia; Gomez-Lorenzo, Maria G. ; Gamo, Francisco Javier ; Winzeler, Elizabeth A.; Fidock, David A. ; Chookajorn, Thanat; Lee, Marcus C. S.

Abstract: In vitro evolution of drug resistance is a powerful approach for identifying antimalarial targets, however, key obstacles to eliciting resistance are the parasite inoculum size and mutation rate. Here we sought to increase parasite genetic diversity to potentiate resistance selections by editing catalytic residues of Plasmodium falciparum DNA polymerase δ. Mutation accumulation assays reveal a ∼5-8 fold elevation in the mutation rate, with an increase of 13-28 fold in drug-pressured lines. Upon challenge with the spiroindolone PfATP4-inhibitor KAE609, high-level resistance is obtained more rapidly and at lower inocula than wild-type parasites. Selections also yield mutants with resistance to an “irresistible” compound, MMV665794 that failed to yield resistance with other strains. We validate mutations in a previously uncharacterised gene, PF3D7_1359900, which we term quinoxaline resistance protein (QRP1), as causal for resistance to MMV665794 and a panel of quinoxaline analogs. The increased genetic repertoire available to this “mutator” parasite can be leveraged to drive P. falciparum resistome discovery.

Pyrrolidine-oxadiazolone conjugate as new organocatalyst for asymmetric aldol condensation

Published in : Synthetic Communications

DOI: 10.1080/00397911.2023.2205593

Authors: Chandan K. Mahato (TCGLS Member),Subhro Mandal,Mrinalkanti Kundu (TCGLS Member)&AnimeshPramanik

Abstract: A proline-based, chiral bi-functional organocatalyst containing both pyrrolidine and oxadiazolone heterocycle, has been successfully applied for stereoselective aldol reactions. The replacement of polar -COOH group of proline with bioisostereoxadiazolone ring provides excellent solubility of this catalyst in various organic solvents compared to low soluble proline. As a result, the organocatalyst effectively catalyzed the asymmetric condensation reaction between differently substituted aromatic aldehydes and various symmetrical and unsymmetrical ketones to produce the corresponding aldol products with excellent stereoselectivities (dr: 97:3, ee>99.9%) at room temperature in open-air.

 7-N-Substituted-3-oxadiazole Quinolones with Potent Antimalarial Activity Target the Cytochrome bc1 Complex 

Published in: ACS Infectious DiseasesVolume: 9Issue: 3Pages: 668-691

DOI: 10.1021/acsinfecdis.2c00607

Authors: Nguyen, William; Dans, Madeline G.; Currie, Iain; Awalt, Jon Kyle ; Bailey, Brodie L.; Lumb, Chris; Ngo, Anna; Favuzza, Paola; Palandri, Josephine; Ramesh, Saishyam; Penington, Jocelyn ; Jarman, Kate E.; Mukherjee, Partha (TCGLS Member); Chakraborty, Arnish (TCGLS Member); Maier, Alexander G.; van Dooren, Giel G.; Papenfuss, Tony; Wittlin, Sergio ; Churchyard, Alisje; Baum, Jake; Winzeler, Elizabeth A. ; Baud, Delphine; Brand, Stephen; Jackson, Paul F.; Cowman, Alan F.; Sleebs, Brad E.

Abstract: The development of new antimalarials is required because of the threat of resistance to current antimalarial therapies. To discover new antimalarial chemotypes, we screened the Janssen Jumpstarter library against the P. falciparum asexual parasite and identified the 7-N-substituted-3-oxadiazole quinolone hit class I [R = pyrrolidin-1-yl, 4-acetylpiperazin-1-yl, azepan-1-yl, etc.]. We established the structure-activity relationship and optimized the antimalarial potency. The optimized analog compound I (R = 4-methylpiperidin-1-yl) showed robust metabolic stability in vitro, although the aqueous solubility was limited. Forward genetic resistance studies uncovered that I (R = 4-methylpiperidin-1-yl) targets the Qo site of cytochrome b (cyt b), an important component of the mitochondrial electron transport chain (ETC) that is essential for pyrimidine biosynthesis and an established antimalarial target. Profiling against drug-resistant parasites confirmed that WJM228 confers resistance to the Qo site but not Qi site mutations, and in a biosensor assay, it was shown to impact the ETC via inhibition of cyt b. Consistent with other cyt b targeted antimalarials, I (R = 4-methylpiperidin-1-yl) prevented pre-erythrocytic parasite and male gamete development and reduced asexual parasitemia in a P. berghei mouse model of malaria. Correcting the limited aqueous solubility and the high susceptibility to cyt b Qo site resistant parasites found in the clinic will be major obstacles in the future development of the 3-oxadiazole quinolone antimalarial class I.

Graphical Abstract:

Optimization of 2,3-Dihydroquinazolinone-3-carboxamides as Antimalarials Targeting PfATP4

Publication: Journal of Medicinal Chemistry

Authors: Ashton, Trent D. ; Dans, Madeline G.; Favuzza, Paola; Ngo, Anna; Lehane, Adele M. ; Zhang, Xinxin; Qiu, Deyun; Chandra Maity, Bikash (TCGLS Member); De, Nirupam (TCGLS Member); Schindler, Kyra A.; Yeo, Tomas; Park, Heekuk; Uhlemann, Anne-Catrin ; Churchyard, Alisje; Baum, Jake; Fidock, David A.; Jarman, Kate E.; Lowes, Kym N.; Baud, Delphine; Brand, Stephen; Jackson, Paul F.; Cowman, Alan F.; Sleebs, Brad E.

Abstract: There is an urgent need to populate the antimalarial clin. portfolio with new candidates because of resistance against frontline antimalarials. To discover new antimalarial chemotypes, we performed a high-throughput screen of the Janssen Jumpstarter library against the Plasmodium falciparum asexual blood-stage parasite and identified the 2,3-dihydroquinazolinone-3-carboxamide scaffold. We defined the SAR and found that 8-substitution on the tricyclic ring system and 3-substitution of the exocyclic arene produced analogs with potent activity against asexual parasites equivalent to clin. used antimalarials. Resistance selection and profiling against drug-resistant parasite strains revealed that this antimalarial chemotype targets PfATP4. Dihydroquinazolinone analogs were shown to disrupt parasite Na+ homeostasis and affect parasite pH, exhibited a fast-to-moderate rate of asexual kill, and blocked gametogenesis, consistent with the phenotype of clin. used PfATP4 inhibitors. Finally, we observed that optimized frontrunner analog WJM-921 demonstrates oral efficacy in a mouse model of malaria.

Graphical Abstract:

Collaborative Virtual Screening Identifies a 2-Aryl-4-aminoquinazoline Series with Efficacy in an In Vivo Model of Trypanosoma cruzi Infection

Authors: Tawaraishi, Taisuke; Ochida, Atsuko; Akao, Yuichiro; Itono, Sachiko; Kamaura, Masahiro; Akther, Thamina; Shimada, Mitsuyuki; Canan, Stacie; Chowdhury, Sanjoy (TCGLS Member); Cao, Yafeng; Condroski, Kevin ; Engkvist, Ola ; Francisco, Amanda; Ghosh, Sunil (TCGLS Member); Kaki, Rina; Kelly, John M.; Kimura, Chiaki; Kogej, Thierry; Nagaoka, Kazuya; Naito, Akira; Pairaudeau, Garry; Radu, Constantin; Roberts, Ieuan; Shum, David; Watanabe, Nao-aki; Xie, Huanxu; Yonezawa, Shuji; Yoshida, Osamu; Yoshida, Ryu; Mowbray, Charles ; Perry, Benjamin

Publication: Journal of Medicinal Chemistry (2023), 66(2), 1221-1238

Abstract: Probing multiple proprietary pharmaceutical libraries in parallel via virtual screening allowed rapid expansion of the structure-activity relationship (SAR) around hit compounds with moderate efficacy against Trypanosoma cruzi, the causative agent of Chagas Disease. A potency-improving scaffold hop, followed by elaboration of the SAR via design guided by the output of the phenotypic virtual screening efforts, identified two promising hit compounds 54 and 85, which were profiled further in pharmacokinetic studies and in an in-vivo model of T. cruzi infection. Compound 85 demonstrated clear reduction of parasitemia in the in-vivo setting, confirming the interest in this series of 2-(pyridin-2-yl)quinazolines as potential anti-trypanosome treatments.

Graphical Abstract:

Exploring a Tetrahydroquinoline Antimalarial Hit from the Medicines for Malaria Pathogen Box and Identification of its Mode of Resistance as PfeEF2

Dr. Benoît Laleu,Kelly Rubiano,Tomas Yeo,Irene Hallyburton,Dr. Mark Anderson,Benigno Crespo-Fernandez,Dr. Francisco-Javier Gamo,Dr. Yevgeniya Antonova-Koch,Dr. Pamela Orjuela-Sanchez,Dr. Sergio Wittlin,Dr. Gouranga P. Jana (TCGLS Member),Dr. Bikash C. Maity (TCGLS Member),Elodie Chenu,Dr. James Duffy,Dr. Peter Sjö,Dr. David Waterson,Prof. Elizabeth Winzeler,Dr. Eric Guantai,Prof. David A. Fidock,Dr. Thomas G. Hansson

Publication: ChemMedChem, e202200393

Abstract:  Toolkit expansion: We report an exploration of the antimalarial compound MMV692140. The mode of resistance was identified as PfeEF2. The structural motif was explored in a chemistry program, resulting in the identification of MMV1919557, an analog with significantly improved antimalarial potency. This new series could provide a tool to further understand the potential of PfeEF2 as a target for malaria treatment

New antimalarial treatments with novel mechanism of action are needed to tackle Plasmodium falciparum infections that are resistant to first-line therapeutics. Here we report the exploration of MMV692140 (2) from the Pathogen Box, a collection of 400 compounds that was made available by Medicines for Malaria Venture (MMV) in 2015. Compound 2 was profiled in in vitro models of malaria and was found to be active against multiple life-cycle stages of Plasmodium parasites. The mode of resistance, and putatively its mode of action, was identified as Plasmodium falciparum translation elongation factor 2 (PfeEF2), which is responsible for the GTP-dependent translocation of the ribosome along mRNA. The compound maintains activity against a series of drug-resistant parasite strains. The structural motif of the tetrahydroquinoline (2) was explored in a chemistry program with its structure-activity relationships examined, resulting in the identification of an analog with 30-fold improvement of antimalarial asexual blood stage potency.

Synthesis, anti-cancer activity and molecular docking studies of new nicotinamide containing EP4 antagonists

Md. Akram Ali (TCGLS Member), Rajib Chakraborty (TCGLS Member), Susanta Kumar Mondal (TCGLS Member). Supriya Bhunia, Sabyasachi Chakraborty (TCGLS Member), Subhas Samanta, Sonali Rudra (TCGLS Member)

Publication: Journal of Molecular Structure Volume 1260, 15 July 2022, 132730

Abstract: Selective binding of the pleiotropic lipid mediator prostanoid Prostaglandin E2 (PGE2) towards the G-protein coupled EP4 receptor has been studied extensively for inflammatory and hyperalgesia models and has been implicated to have significant potential for the treatment of various forms of cancers. Interest of nicotinamides as EP4 antagonists for oncology research, led us to synthesize a small set of molecules using the nicotinamide derivative AAT-008 (1) as our starting point for design. Subtle changes by replacing the hydrogen bond accepting bi-aryl-ether moiety in (1) to hydrogen bond donating bi-aryl-amino moiety and thereafter modifications on the substituents in the bi-aryl ring systems, carboxyl and the amino groups enabled us to identify a modestly potent new EP4 antagonist compound 14 with IC50 = 0.543 ± 0.148 μM (n = 6). Compound 14 was found to be stable in ADME assays and had reasonably good solubility. The interplay of electronic parameters such as lipohilicity and polarity of the compounds did not seem to play a significant role in deriving the EP4 antagonism potency for these compounds. Thus, molecular docking studies were carried out to understand the structure activity relationships (SAR). The trend in activity range of the synthesized compounds and the lower EP4 activity of compound 14 in contrast to compound 1 was explained with aid of molecular docking studies that supported our experimental potency results also. Preliminary screening of compounds 1 and 14 for oncology showed weak activity at a modest dose of 500 μM in breast cancer cells (MDA-MB-231) and moderately significant activity in colon cancer cells (HCT-116) cytotoxicity assays. Since, there was relatively higher cytotoxic activity in colon cancer cell lines, the cytotoxic effects of these two compounds were further evaluated under PGE2 induced conditions in two colon cancer cell lines: HCT-116 cells (IC50 values of 46 µM and 50 µM for compounds 1 and 14, respectively) and HT-29 cells (IC50 values of 37 µM and 4.5 µM for compounds 1 and 14, respectively) which signifies the possible relevance of the prostanoid inhibition pathway and its interference through the PGE2 induced oncogenic pathway.

Bioinspired Synthesis of Pinoxaden Metabolites Using a Site-Selective C–H Oxidation Strategy

Sameer Tyagi, Bruce P. McKillican, Tolani K. Salvador, Moses G. Gichinga, William J. Eberle, Russell Viner, Katarina J. Makaravage, Trey S. Johnson, C. Adam Russell, and Subho Roy (TCGLS Member)

Publication: J. Org. Chem. 2022, 87, 9, 6202–6211

Abstract: A bioinspired synthesis of Pinoxaden metabolites 2–5 is described herein. A site-selective C–H oxidation strategy validated by density functional theory (DFT) calculations was devised for preparing metabolites 2–4. Oxidation of the benzylic C–H bond in tertiary alcohol 7 using K2S2O8 and catalytic AgNO3 formed the desired metabolite 2 that enabled access to metabolites 3 and 4 in a single step. Unlike most metal/persulfate-catalyzed transformations reported for the C–C and C–O bond formation reactions wherein the metal acts as a catalyst, we propose that Ag(I)/K2S2O8 plays the role of an initiator in the oxidation of intermediate 7 to 2. Metabolite 2 was subjected to a ruthenium tetroxide-mediated C–H oxidation to form metabolites 3 and 4 as a mixture that were purified to isolate pure standards of these metabolites. Metabolite 5 was synthesized from readily available advanced intermediate 9via a House–Meinwald-type rearrangement in one step using a base.

Diastereo- and regioselective petasis aryl and allyl boration of ninhydrins towards synthesis of functionalized indene-diones and dihydrobenzoindeno-oxazin-ones

Ayon Sengupta (TCGLS Member), Suvendu Maity, Pinaki Saha, Prasanta Ghosh, Sonali Rudra (TCGLS Member), Chhanda Mukhopadhyay

Publication: Mol Divers. 2022 Aug 1. doi: 10.1007/s11030-022-10496-4. Online ahead of print

Abstract: Petasis aryl and allyl borations were accomplished using substituted ninhydrins, boronic acids or 2-allyl-4,4,5,5-tetramethyl-1,3,2-dioxaborolane and 1,2-aminophenols in Hexafluoroisopropanol (HFIP) without any catalysts to synthesize different aryl and allyl derivatives of ninhydrins. The nature of substitution in the boronic acids and 1,2-amino phenols was the key factor in determining the diastereo-regioselectivity and the type of product distributions. The products were isolated and characterized by HMBC, HSQC, 1H, 13C NMR experiments and X-ray single crystallographic analysis. A probable reaction pathway involves in situ formation of acyclic and cyclic ninhydrin-amino alcohol adducts, with the positioned hydroxyl group determining the stereo-regioselective outcome via tetracoordinated boron intermediates. A metal free diastereo- and regioselective Petasis aryl and allyl boration of ninhydrins

Identification of 5-(3-(methylsulfonyl)phenyl)-3-(4-(methylsulfonyl)phenyl)-3H-imidazo[4,5-b]pyridine as novel orally bioavailable and metabolically stable antimalarial compound for further exploration

Kundu Mrinalkanti (TCGLS Member); Dutta Aditi (TCGLS Member); Mal Sajal K (TCGLS Member); Karmakar Shouvik (TCGLS Member); Mandal Aritra (TCGLS Member); Mondal Susanta K (TCGLS Member); Kumar Sanjay (TCGLS Member); Saha Soumya (TCGLS Member); Pradhan Subhankar (TCGLS Member); Sarkar Ratul (TCGLS Member); Chakrabarti Monali (TCGLS Member); Malik Pradip K (TCGLS Member); Banerjee Manish (TCGLS Member); Roy Kuldeep K

Publication: Chemical biology & drug design, ASAP

Abstract: Malaria continues to be a significant public health problem threatened by the emergence and spread of resistance to artemisinin-based combination therapies and marked half a million deaths in 2016. A new imidazopyridine chemotype has been envisaged through scaffold-hopping approach combined with docking studies for putative binding interactions with Plasmodium falciparum phosphatidylinositol-4-kinase (PfPI4K) target. The docking results steered to the synthesis of compound 1 [5-(3-(methylsulfonyl)phenyl)-3-(4-(methylsulfonyl)phenyl)-3H-imidazo[4,5-b]pyridine] followed by the in vitro screening for antiplasmodial activity and ADME-PK studies. Combined with potent antimalarial activity of compound 1 (Pf3D7 IC50 = 29 nM) with meager in vitro intrinsic clearance, moderate plasma-protein binding and acceptable permeability, compound 1 displayed sustained exposure and high oral bioavailability in mice and can thus have the potential as next generation PI4K inhibitor for in vivo studies.