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

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          Abstract

          There is an urgent need to populate the antimalarial clinical 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 analogues with potent activity against asexual parasites equivalent to clinically used antimalarials. Resistance selection and profiling against drug-resistant parasite strains revealed that this antimalarial chemotype targets PfATP4. Dihydroquinazolinone analogues 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 clinically used PfATP4 inhibitors. Finally, we observed that optimized frontrunner analogue WJM-921 demonstrates oral efficacy in a mouse model of malaria.

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          A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.

          We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants in genome sequences. Once a genome is sequenced, SnpEff annotates variants based on their genomic locations and predicts coding effects. Annotated genomic locations include intronic, untranslated region, upstream, downstream, splice site, or intergenic regions. Coding effects such as synonymous or non-synonymous amino acid replacement, start codon gains or losses, stop codon gains or losses, or frame shifts can be predicted. Here the use of SnpEff is illustrated by annotating ~356,660 candidate SNPs in ~117 Mb unique sequences, representing a substitution rate of ~1/305 nucleotides, between the Drosophila melanogaster w(1118); iso-2; iso-3 strain and the reference y(1); cn(1) bw(1) sp(1) strain. We show that ~15,842 SNPs are synonymous and ~4,467 SNPs are non-synonymous (N/S ~0.28). The remaining SNPs are in other categories, such as stop codon gains (38 SNPs), stop codon losses (8 SNPs), and start codon gains (297 SNPs) in the 5'UTR. We found, as expected, that the SNP frequency is proportional to the recombination frequency (i.e., highest in the middle of chromosome arms). We also found that start-gain or stop-lost SNPs in Drosophila melanogaster often result in additions of N-terminal or C-terminal amino acids that are conserved in other Drosophila species. It appears that the 5' and 3' UTRs are reservoirs for genetic variations that changes the termini of proteins during evolution of the Drosophila genus. As genome sequencing is becoming inexpensive and routine, SnpEff enables rapid analyses of whole-genome sequencing data to be performed by an individual laboratory.
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            OLEX2: a complete structure solution, refinement and analysis program

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              Artemisinin resistance in Plasmodium falciparum malaria.

              Artemisinin-based combination therapies are the recommended first-line treatments of falciparum malaria in all countries with endemic disease. There are recent concerns that the efficacy of such therapies has declined on the Thai-Cambodian border, historically a site of emerging antimalarial-drug resistance. In two open-label, randomized trials, we compared the efficacies of two treatments for uncomplicated falciparum malaria in Pailin, western Cambodia, and Wang Pha, northwestern Thailand: oral artesunate given at a dose of 2 mg per kilogram of body weight per day, for 7 days, and artesunate given at a dose of 4 mg per kilogram per day, for 3 days, followed by mefloquine at two doses totaling 25 mg per kilogram. We assessed in vitro and in vivo Plasmodium falciparum susceptibility, artesunate pharmacokinetics, and molecular markers of resistance. We studied 40 patients in each of the two locations. The overall median parasite clearance times were 84 hours (interquartile range, 60 to 96) in Pailin and 48 hours (interquartile range, 36 to 66) in Wang Pha (P<0.001). Recrudescence confirmed by means of polymerase-chain-reaction assay occurred in 6 of 20 patients (30%) receiving artesunate monotherapy and 1 of 20 (5%) receiving artesunate-mefloquine therapy in Pailin, as compared with 2 of 20 (10%) and 1 of 20 (5%), respectively, in Wang Pha (P=0.31). These markedly different parasitologic responses were not explained by differences in age, artesunate or dihydroartemisinin pharmacokinetics, results of isotopic in vitro sensitivity tests, or putative molecular correlates of P. falciparum drug resistance (mutations or amplifications of the gene encoding a multidrug resistance protein [PfMDR1] or mutations in the gene encoding sarco-endoplasmic reticulum calcium ATPase6 [PfSERCA]). Adverse events were mild and did not differ significantly between the two treatment groups. P. falciparum has reduced in vivo susceptibility to artesunate in western Cambodia as compared with northwestern Thailand. Resistance is characterized by slow parasite clearance in vivo without corresponding reductions on conventional in vitro susceptibility testing. Containment measures are urgently needed. (ClinicalTrials.gov number, NCT00493363, and Current Controlled Trials number, ISRCTN64835265.) 2009 Massachusetts Medical Society
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                Author and article information

                Journal
                J Med Chem
                J Med Chem
                jm
                jmcmar
                Journal of Medicinal Chemistry
                American Chemical Society
                0022-2623
                1520-4804
                22 February 2023
                09 March 2023
                : 66
                : 5
                : 3540-3565
                Affiliations
                []The Walter and Eliza Hall Institute of Medical Research , Parkville 3052, Australia
                []Department of Medical Biology, The University of Melbourne , Parkville 3010, Australia
                [§ ]Research School of Biology, Australian National University , Canberra 2601, Australia
                []TCG Lifesciences Pvt. Ltd. , Saltlake Sec-V, Kolkata 700091, West Bengal, India
                []Department of Microbiology & Immunology, Columbia University, Irving Medical Center , New York, New York 10032, United States
                [# ]Department of Life Sciences, Imperial College London , South Kensington SW7 2AZ U.K.
                []School of Biomedical Sciences, University of New South Wales , Sydney 2031, Australia
                []Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University, Irving Medical Center , New York, New York 10032, United States
                []Medicines for Malaria Venture, ICC , Route de Pré-Bois 20, 1215 Geneva, Switzerland
                []Global Public Health, Janssen R&D LLC , La Jolla, California 92121, United States
                Author notes
                [* ]Email: sleebs@ 123456wehi.edu.au . Tel: 61 3 9345 2718.
                Author information
                https://orcid.org/0000-0002-6707-6064
                https://orcid.org/0000-0002-0050-9101
                https://orcid.org/0000-0002-9798-4768
                https://orcid.org/0000-0001-9117-1048
                Article
                10.1021/acs.jmedchem.2c02092
                10009754
                36812492
                eff15139-d926-4616-956b-8d71d8d44f68
                © 2023 The Authors. Published by American Chemical Society

                Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works ( https://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 21 December 2022
                Funding
                Funded by: Wellcome, doi 10.13039/100010269;
                Award ID: 100993/Z/13/Z
                Funded by: Medicines for Malaria Venture, doi 10.13039/501100004167;
                Award ID: RD-18-0003
                Funded by: Medicines for Malaria Venture, doi 10.13039/501100004167;
                Award ID: RD-08-2800
                Funded by: Medicines for Malaria Venture, doi 10.13039/501100004167;
                Award ID: RD-08-0015
                Funded by: National Health and Medical Research Council, doi 10.13039/501100000925;
                Award ID: 1135421
                Categories
                Article
                Custom metadata
                jm2c02092
                jm2c02092

                Pharmaceutical chemistry
                Pharmaceutical chemistry

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