1
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Baumann HM, Mobley DL. Impact of protein conformations on binding free energy calculations in the beta-secretase 1 system. J Comput Chem 2024; 45:2024-2033. [PMID: 38725239 PMCID: PMC11236511 DOI: 10.1002/jcc.27365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/13/2024] [Accepted: 03/24/2024] [Indexed: 07/11/2024]
Abstract
In binding free energy calculations, simulations must sample all relevant conformations of the system in order to obtain unbiased results. For instance, different ligands can bind to different metastable states of a protein, and if these protein conformational changes are not sampled in relative binding free energy calculations, the contribution of these states to binding is not accounted for and thus calculated binding free energies are inaccurate. In this work, we investigate the impact of different beta-sectretase 1 (BACE1) protein conformations obtained from x-ray crystallography on the binding of BACE1 inhibitors. We highlight how these conformational changes are not adequately sampled in typical molecular dynamics simulations. Furthermore, we show that insufficient sampling of relevant conformations induces substantial error in relative binding free energy calculations, as judged by a variation in calculated relative binding free energies up to 2 kcal/mol depending on the starting protein conformation. These results emphasize the importance of protein conformational sampling and pose this BACE1 system as a challenge case for further method development in the area of enhanced protein conformational sampling, either in combination with binding calculations or as an endpoint correction.
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Affiliation(s)
- Hannah M Baumann
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, California, USA
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2
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Lawong A, Gahalawat S, Ray S, Ho N, Han Y, Ward KE, Deng X, Chen Z, Kumar A, Xing C, Hosangadi V, Fairhurst KJ, Tashiro K, Liszczak G, Shackleford DM, Katneni K, Chen G, Saunders J, Crighton E, Casas A, Robinson JJ, Imlay LS, Zhang X, Lemoff A, Zhao Z, Angulo-Barturen I, Jiménez-Díaz MB, Wittlin S, Campbell SF, Fidock DA, Laleu B, Charman SA, Ready JM, Phillips MA. Identification of potent and reversible piperidine carboxamides that are species-selective orally active proteasome inhibitors to treat malaria. Cell Chem Biol 2024:S2451-9456(24)00278-2. [PMID: 39084225 DOI: 10.1016/j.chembiol.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/08/2024] [Accepted: 07/03/2024] [Indexed: 08/02/2024]
Abstract
Malaria remains a global health concern as drug resistance threatens treatment programs. We identified a piperidine carboxamide (SW042) with anti-malarial activity by phenotypic screening. Selection of SW042-resistant Plasmodium falciparum (Pf) parasites revealed point mutations in the Pf_proteasome β5 active-site (Pfβ5). A potent analog (SW584) showed efficacy in a mouse model of human malaria after oral dosing. SW584 had a low propensity to generate resistance (minimum inoculum for resistance [MIR] >109) and was synergistic with dihydroartemisinin. Pf_proteasome purification was facilitated by His8-tag introduction onto β7. Inhibition of Pfβ5 correlated with parasite killing, without inhibiting human proteasome isoforms or showing cytotoxicity. The Pf_proteasome_SW584 cryoelectron microscopy (cryo-EM) structure showed that SW584 bound non-covalently distal from the catalytic threonine, in an unexplored pocket at the β5/β6/β3 subunit interface that has species differences between Pf and human proteasomes. Identification of a reversible, species selective, orally active series with low resistance propensity provides a path for drugging this essential target.
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Affiliation(s)
- Aloysus Lawong
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Suraksha Gahalawat
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Sneha Ray
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Nhi Ho
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Yan Han
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Kurt E Ward
- Department of Microbiology and Immunology, and Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiaoyi Deng
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Ashwani Kumar
- Department of Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Chao Xing
- Department of Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA; Department of Bioinformatics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Varun Hosangadi
- Department of Microbiology and Immunology, and Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kate J Fairhurst
- Department of Microbiology and Immunology, and Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kyuto Tashiro
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Glen Liszczak
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - David M Shackleford
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Jessica Saunders
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Elly Crighton
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Arturo Casas
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Joshua J Robinson
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Leah S Imlay
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Xiaoyu Zhang
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Zhiyu Zhao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Iñigo Angulo-Barturen
- The Art of Discovery, Biscay Science and Technology Park, Astrondo Bidea, BIC Bizkaia Bd 612, Derio, 48160 Bizkaia, Basque Country, Spain
| | - María Belén Jiménez-Díaz
- The Art of Discovery, Biscay Science and Technology Park, Astrondo Bidea, BIC Bizkaia Bd 612, Derio, 48160 Bizkaia, Basque Country, Spain
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland; University of Basel Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | | | - David A Fidock
- Department of Microbiology and Immunology, and Columbia University Irving Medical Center, New York, NY 10032, USA; Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Benoît Laleu
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Joseph M Ready
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.
| | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.
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3
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Bagratee T, Prawlall R, Ndlovu T, Sibisi S, Ndadane S, Shaik BB, Palkar MB, Gampa R, Karpoormath R. Exploring the Recent Pioneering Developments of Small Molecules in Antimalarial Drug Armamentarium: A Chemistry Prospective Appraisal. Chem Biodivers 2024:e202400460. [PMID: 38759144 DOI: 10.1002/cbdv.202400460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 05/19/2024]
Abstract
Malaria is a very destructive and lethal parasitic disease that causes significant mortality worldwide, resulting in the loss of millions of lives annually. It is an infectious disease transmitted by mosquitoes, which is caused by different species of the parasite protozoan belonging to the genus Plasmodium. The uncontrolled intake of antimalarial drugs often employed in clinical settings has resulted in the emergence of numerous strains of plasmodium that are resistant to these drugs, including multidrug-resistant strains. This resistance significantly diminishes the effectiveness of many primary drugs used in the treatment of malaria. Hence, there is an urgent need for developing unique classes of antimalarial drugs that function with distinct mechanisms of action. In this context, the design and development of hybrid compounds that combine pharmacophoric properties from different lead molecules into a single unit gives a unique perspective towards further development of malaria drugs in the next generation. In recent years, the field of medicinal chemistry has made significant efforts resulting in the discovery and synthesis of numerous small novel compounds that exhibit potent antimalarial properties, while also demonstrating reduced toxicity and desirable efficacy. In light of this, we have reviewed the progress of hybrid antimalarial agents from 2021 up to the present. This manuscript presents a comprehensive overview of the latest advancements in the medicinal chemistry pertaining to small molecules, with a specific focus on their potential as antimalarial agents. As possible antimalarial drugs that might target both the dual stage and multi-stage stages of the parasite life cycle, these small hybrid molecules have been studied. This review explores a variety of physiologically active compounds that have been described in the literature in order to lay a strong foundation for the logical design and eventual identification of antimalarial drugs based on lead frameworks.
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Affiliation(s)
- Tameika Bagratee
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa
| | - Ritika Prawlall
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa
| | - Thabani Ndlovu
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa
| | - Sinqobile Sibisi
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa
| | - Sisa Ndadane
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa
| | - Baji Baba Shaik
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa
| | - Mahesh B Palkar
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa
- Department of Pharmaceutical Chemistry, SVKM's NMIMS, Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, Vile Parle (West), Mumbai, 400056, Maharashtra, India
| | - Raghavachary Gampa
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban, 4000, South Africa
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4
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Sharma M, Pandey V, Poli G, Tuccinardi T, Lolli ML, Vyas VK. A comprehensive review of synthetic strategies and SAR studies for the discovery of PfDHODH inhibitors as antimalarial agents. Part 1: triazolopyrimidine, isoxazolopyrimidine and pyrrole-based (DSM) compounds. Bioorg Chem 2024; 146:107249. [PMID: 38493638 DOI: 10.1016/j.bioorg.2024.107249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/10/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024]
Abstract
One of the deadliest infectious diseases, malaria, still has a significant impact on global morbidity and mortality. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) catalyzes the fourth step in de novo pyrimidine nucleotide biosynthesis and has been clinically validated as an innovative and promising target for the development of novel targeted antimalarial drugs. PfDHODH inhibitors have the potential to significantly slow down parasite growth at the blood and liver stages. Several PfDHODH inhibitors based on various scaffolds have been explored over the past two decades. Among them, triazolopyrimidines, isoxazolopyrimidines, and pyrrole-based derivatives known as DSM compounds showed tremendous potential as novel antimalarial agents, and one of the triazolopyrimidine-based compounds (DSM265) was able to reach phase IIa clinical trials. DSM compounds were synthesized as PfDHODH inhibitors with various substitutions based on structure-guided medicinal chemistry approaches and further optimised as well. For the first time, this review provides an overview of all the synthetic approaches used for the synthesis, alternative synthetic routes, and novel strategies involving various catalysts and chemical reagents that have been used to synthesize DSM compounds. We have also summarized SAR study of all these PfDHODH inhibitors. In an attempt to assist readers, scientists, and researchers involved in the development of new PfDHODH inhibitors as antimalarials, this review provides accessibility of all synthetic techniques and SAR studies of the most promising triazolopyrimidines, isoxazolopyrimidines, and pyrrole-based PfDHODH inhibitors.
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Affiliation(s)
- Manmohan Sharma
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad 382481, India
| | - Vinita Pandey
- MIT College of Pharmacy, Ramganga Vihar, Phase-II, Moradabad, UP-244001, India
| | - Giulio Poli
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Marco L Lolli
- Department of Drug Science and Technology, University of Turin, Via P. Giuria 9, 10125 - Turin, Italy
| | - Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad 382481, India.
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5
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Cheuka PM, Njaria P, Mayoka G, Funjika E. Emerging Drug Targets for Antimalarial Drug Discovery: Validation and Insights into Molecular Mechanisms of Function. J Med Chem 2024; 67:838-863. [PMID: 38198596 DOI: 10.1021/acs.jmedchem.3c01828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Approximately 619,000 malaria deaths were reported in 2021, and resistance to recommended drugs, including artemisinin-combination therapies (ACTs), threatens malaria control. Treatment failure with ACTs has been found to be as high as 93% in northeastern Thailand, and parasite mutations responsible for artemisinin resistance have already been reported in some African countries. Therefore, there is an urgent need to identify alternative treatments with novel targets. In this Perspective, we discuss some promising antimalarial drug targets, including enzymes involved in proteolysis, DNA and RNA metabolism, protein synthesis, and isoprenoid metabolism. Other targets discussed are transporters, Plasmodium falciparum acetyl-coenzyme A synthetase, N-myristoyltransferase, and the cyclic guanosine monophosphate-dependent protein kinase G. We have outlined mechanistic details, where these are understood, underpinning the biological roles and hence druggability of such targets. We believe that having a clear understanding of the underlying chemical interactions is valuable to medicinal chemists in their quest to design appropriate inhibitors.
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Affiliation(s)
- Peter Mubanga Cheuka
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
| | - Paul Njaria
- Department of Pharmacognosy and Pharmaceutical Chemistry, Kenyatta University, P.O. Box 14548-00400, Nairobi 00100, Kenya
| | - Godfrey Mayoka
- Department of Pharmacology and Pharmacognosy, School of Pharmacy, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi 00100, Kenya
| | - Evelyn Funjika
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
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6
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Liu S, Ebel ER, Luniewski A, Zulawinska J, Simpson ML, Kim J, Ene N, Braukmann TWA, Congdon M, Santos W, Yeh E, Guler JL. Direct long read visualization reveals metabolic interplay between two antimalarial drug targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528367. [PMID: 36824743 PMCID: PMC9948948 DOI: 10.1101/2023.02.13.528367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Increases in the copy number of large genomic regions, termed genome amplification, are an important adaptive strategy for malaria parasites. Numerous amplifications across the Plasmodium falciparum genome contribute directly to drug resistance or impact the fitness of this protozoan parasite. During the characterization of parasite lines with amplifications of the dihydroorotate dehydrogenase (DHODH) gene, we detected increased copies of an additional genomic region that encompassed 3 genes (~5 kb) including GTP cyclohydrolase I (GCH1 amplicon). While this gene is reported to increase the fitness of antifolate resistant parasites, GCH1 amplicons had not previously been implicated in any other antimalarial resistance context. Here, we further explored the association between GCH1 and DHODH copy number. Using long read sequencing and single read visualization, we directly observed a higher number of tandem GCH1 amplicons in parasites with increased DHODH copies (up to 9 amplicons) compared to parental parasites (3 amplicons). While all GCH1 amplicons shared a consistent structure, expansions arose in 2-unit steps (from 3 to 5 to 7, etc copies). Adaptive evolution of DHODH and GCH1 loci was further bolstered when we evaluated prior selection experiments; DHODH amplification was only successful in parasite lines with pre-existing GCH1 amplicons. These observations, combined with the direct connection between metabolic pathways that contain these enzymes, lead us to propose that the GCH1 locus is beneficial for the fitness of parasites exposed to DHODH inhibitors. This finding highlights the importance of studying variation within individual parasite genomes as well as biochemical connections of drug targets as novel antimalarials move towards clinical approval.
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Affiliation(s)
- Shiwei Liu
- University of Virginia, Department of Biology, Charlottesville, VA, USA
- Current affiliation: Indiana University School of Medicine, Indianapolis, IN, USA
| | - Emily R. Ebel
- Stanford, Departments of Pediatrics and Microbiology & Immunology, Stanford, CA, USA
| | | | - Julia Zulawinska
- University of Virginia, Department of Biology, Charlottesville, VA, USA
| | | | - Jane Kim
- University of Virginia, Department of Biology, Charlottesville, VA, USA
| | - Nnenna Ene
- University of Virginia, Department of Biology, Charlottesville, VA, USA
| | | | - Molly Congdon
- Virginia Tech, Department of Chemistry, Blacksburg, VA, USA
| | - Webster Santos
- Virginia Tech, Department of Chemistry, Blacksburg, VA, USA
| | - Ellen Yeh
- Stanford University, Departments of Pathology and Microbiology & Immunology, Stanford, CA, USA
| | - Jennifer L. Guler
- University of Virginia, Department of Biology, Charlottesville, VA, USA
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7
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Siqueira-Neto JL, Wicht KJ, Chibale K, Burrows JN, Fidock DA, Winzeler EA. Antimalarial drug discovery: progress and approaches. Nat Rev Drug Discov 2023; 22:807-826. [PMID: 37652975 PMCID: PMC10543600 DOI: 10.1038/s41573-023-00772-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 09/02/2023]
Abstract
Recent antimalarial drug discovery has been a race to produce new medicines that overcome emerging drug resistance, whilst considering safety and improving dosing convenience. Discovery efforts have yielded a variety of new molecules, many with novel modes of action, and the most advanced are in late-stage clinical development. These discoveries have led to a deeper understanding of how antimalarial drugs act, the identification of a new generation of drug targets, and multiple structure-based chemistry initiatives. The limited pool of funding means it is vital to prioritize new drug candidates. They should exhibit high potency, a low propensity for resistance, a pharmacokinetic profile that favours infrequent dosing, low cost, preclinical results that demonstrate safety and tolerability in women and infants, and preferably the ability to block Plasmodium transmission to Anopheles mosquito vectors. In this Review, we describe the approaches that have been successful, progress in preclinical and clinical development, and existing challenges. We illustrate how antimalarial drug discovery can serve as a model for drug discovery in diseases of poverty.
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Affiliation(s)
| | - Kathryn J Wicht
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
| | - Kelly Chibale
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
| | | | - David A Fidock
- Department of Microbiology and Immunology and Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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8
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Dhawale SA, Bhosle P, Mahajan S, Patil G, Gawale S, Ghodke M, Tapadiya G, Ansari A. Dual targeting in prostate cancer with phytoconstituents as a potent lead: a computational approach for novel drug discovery. J Biomol Struct Dyn 2023:1-14. [PMID: 37649379 DOI: 10.1080/07391102.2023.2251059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023]
Abstract
Prostate Cancer (PCa) is an abnormal cell growth within the prostate. This condition is the second most widespread malignancy in elderly males and one of the most frequently diagnosed life-threatening conditions. The Androgen receptor signaling pathway played a crucial role in the initiation and spread to increase the risk of PCa. Hence, targeting the AR receptor signaling pathway is a key strategy for a therapeutic plan for PCa. Our study focuses on recognizing potential inhibitors for dual targeting in PCa by using the in-silico approach. In this study, we target the two enzymes that are CYP17A1 (3RUK) and 5α-reductase (3G1R) responsible for PCa, with the help of phytoconstituents. The natural plant contains various phytochemical types produced from secondary metabolites and used as a medical treatment. The in-silico investigation of phytoconstituents and enzymes was done by approaching molecular docking, ADMET analysis, and high-level molecular dynamic simulation used to assess the stability and binding affinities of the protein-ligand complex. Some phytoconstituents, such as Peonidin, Pelargonidin, Malvidin and Berberine show complex has good molecular interaction with protein. The reliability of the docking scores was examined using a molecular dynamic simulation, which revealed that the complex remained stable throughout the simulation, which ranged from 0 to 200 ns. The selected hits may be effective against CYP17A1 (3RUK) and 5α-reductase (3G1R) (PCa) using a computer-aided drug design (CADD) method, which further enables researchers for upcoming in-vivo and in-vitro research, according to our in-silico approach.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sachin A Dhawale
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, India
| | - Pallavi Bhosle
- Pharmacology, Shrinath College of Pharmacy, Aurangabad, India
| | | | - Geetanjali Patil
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, India
| | - Sachin Gawale
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, India
| | - Mangesh Ghodke
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, India
| | - Ganesh Tapadiya
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, India
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9
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Vyas VK, Shukla T, Sharma M. Medicinal chemistry approaches for the discovery of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors as antimalarial agents. Future Med Chem 2023; 15:1295-1321. [PMID: 37551689 DOI: 10.4155/fmc-2023-0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023] Open
Abstract
Malaria is a severe human disease and a global health problem because of drug-resistant strains. Drugs reported to prevent the growth of Plasmodium parasites target various phases of the parasites' life cycle. Antimalarial drugs can inhibit key enzymes that are responsible for the cellular growth and development of parasites. Plasmodium falciparum dihydroorotate dehydrogenase is one such enzyme that is necessary for de novo pyrimidine biosynthesis. This review focuses on various medicinal chemistry approaches used for the discovery and identification of selective P. falciparum dihydroorotate dehydrogenase inhibitors as antimalarial agents. This comprehensive review discusses recent advances in the selective therapeutic activity of distinct chemical classes of compounds as P. falciparum dihydroorotate dehydrogenase inhibitors and antimalarial drugs.
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Affiliation(s)
- Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Tanvi Shukla
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Manmohan Sharma
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
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10
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Liu L, Bulla LA. Cell death signaling in Anopheles gambiae initiated by Bacillus thuringiensis Cry4B toxin involves Na +/K + ATPase. Exp Biol Med (Maywood) 2023; 248:1191-1205. [PMID: 37642306 PMCID: PMC10621475 DOI: 10.1177/15353702231188072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/10/2023] [Indexed: 08/31/2023] Open
Abstract
Identifying the mechanisms by which bacterial pathogens kill host cells is fundamental to understanding how to control and prevent human and animal disease. In the case of Bacillus thuringiensis (Bt), such knowledge is critical to using the bacterium to kill insect vectors that transmit human and animal disease. For the Cry4B toxin produced by Bt, its capacity to kill Anopheles gambiae, the primary mosquito vector of malaria, is the consequence of a variety of signaling activities. We show here that Cry4B, acting as first messenger, binds specifically to the bitopic cadherin BT-R3 G-protein-coupled receptor (GPCR) localized in the midgut of A. gambiae, activating the downstream second messenger cyclic adenosine monophosphate (cAMP). The direct result of the Cry4B-BT-R3 binding is the release of αs from the heterotrimeric αβγ-G-protein complex and its activation of adenylyl cyclase (AC). The upshot is an increased level of cAMP, which activates protein kinase A (PKA). The functional impact of cAMP-PKA signaling is the stimulation of Na+/K+-ATPase (NKA) which serves as an Na+/K+ pump to maintain proper gradients of extracellular Na+ and intracellular K+. Increased level of cAMP amplifies NKA and upsets normal ion concentration gradients. NKA, as a scaffolding protein, accelerates the first messenger signal to the nucleus, generating additional BT-R3 molecules and promoting their exocytotic trafficking to the cell membrane. Accumulation of BT-R3 on the cell surface facilitates recruitment of additional toxin molecules which, in turn, amplify the original signal in a cascade-like manner. This report provides the first evidence of a bacterial toxin using NKA via AC/PKA signaling to execute cell death.
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Affiliation(s)
- Li Liu
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080-3021 USA
| | - Lee A Bulla
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080-3021 USA
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11
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Singh DK, Kumar R. Clauson-Kaas pyrrole synthesis using diverse catalysts: a transition from conventional to greener approach. Beilstein J Org Chem 2023; 19:928-955. [PMID: 37404802 PMCID: PMC10315892 DOI: 10.3762/bjoc.19.71] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/14/2023] [Indexed: 07/06/2023] Open
Abstract
Pyrrole is an important aromatic heterocyclic scaffold found in many natural products and predominantly used in pharmaceuticals. Continuous efforts are being made to design and synthesize various pyrrole derivatives using different synthetic procedures. Among them, the Clauson-Kaas reaction is a very old and well-known method for synthesizing a large number of N-substituted pyrroles. In recent years, due to global warming and environmental concern, research laboratories and pharmaceutical industries around the world are searching for more environmentally friendly reaction conditions for synthesizing compounds. As a result, this review describes the use of various eco-friendly greener protocols to synthesize N-substituted pyrroles. This synthesis involves the reaction of various aliphatic/aromatic primary amines, and sulfonyl primary amines with 2,5-dimethoxytetrahydrofuran in the presence of numerous acid catalysts and transition metal catalysts. The goal of this review is to summarize the synthesis of various N-substituted pyrrole derivatives using a modified Clauson-Kaas reaction under diverse conventional and greener reaction conditions.
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Affiliation(s)
- Dileep Kumar Singh
- Department of Chemistry, Bipin Bihari College, Affiliated to Bundelkhand University, Jhansi-284001, Uttar Pradesh, India
| | - Rajesh Kumar
- P.G. Department of Chemistry, R. D. S. College, B. R. A. Bihar University, Muzaffarpur-842002, Bihar, India
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12
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Kreutzfeld O, Tumwebaze PK, Okitwi M, Orena S, Byaruhanga O, Katairo T, Conrad MD, Rasmussen SA, Legac J, Aydemir O, Giesbrecht D, Forte B, Campbell P, Smith A, Kano H, Nsobya SL, Blasco B, Duffey M, Bailey JA, Cooper RA, Rosenthal PJ. Susceptibility of Ugandan Plasmodium falciparum Isolates to the Antimalarial Drug Pipeline. Microbiol Spectr 2023; 11:e0523622. [PMID: 37158739 PMCID: PMC10269555 DOI: 10.1128/spectrum.05236-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/10/2023] [Indexed: 05/10/2023] Open
Abstract
Malaria, especially Plasmodium falciparum infection, remains an enormous problem, and its treatment and control are seriously challenged by drug resistance. New antimalarial drugs are needed. To characterize the Medicines for Malaria Venture pipeline of antimalarials under development, we assessed the ex vivo drug susceptibilities to 19 compounds targeting or potentially impacted by mutations in P. falciparum ABC transporter I family member 1, acetyl-CoA synthetase, cytochrome b, dihydroorotate dehydrogenase, elongation factor 2, lysyl-tRNA synthetase, phenylalanyl-tRNA synthetase, plasmepsin X, prodrug activation and resistance esterase, and V-type H+ ATPase of 998 fresh P. falciparum clinical isolates collected in eastern Uganda from 2015 to 2022. Drug susceptibilities were assessed by 72-h growth inhibition (half-maximum inhibitory concentration [IC50]) assays using SYBR green. Field isolates were highly susceptible to lead antimalarials, with low- to midnanomolar median IC50s, near values previously reported for laboratory strains, for all tested compounds. However, outliers with decreased susceptibilities were identified. Positive correlations between IC50 results were seen for compounds with shared targets. We sequenced genes encoding presumed targets to characterize sequence diversity, search for polymorphisms previously selected with in vitro drug pressure, and determine genotype-phenotype associations. We identified many polymorphisms in target genes, generally in <10% of isolates, but none were those previously selected in vitro with drug pressure, and none were associated with significantly decreased ex vivo drug susceptibility. Overall, Ugandan P. falciparum isolates were highly susceptible to 19 compounds under development as next-generation antimalarials, consistent with a lack of preexisting or novel resistance-conferring mutations in circulating Ugandan parasites. IMPORTANCE Drug resistance necessitates the development of new antimalarial drugs. It is important to assess the activities of compounds under development against parasites now causing disease in Africa, where most malaria cases occur, and to determine if mutations in these parasites may limit the efficacies of new agents. We found that African isolates were generally highly susceptible to the 19 studied lead antimalarials. Sequencing of the presumed drug targets identified multiple mutations in these genes, but these mutations were generally not associated with decreased antimalarial activity. These results offer confidence that the activities of the tested antimalarial compounds now under development will not be limited by preexisting resistance-mediating mutations in African malaria parasites.
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Affiliation(s)
- Oriana Kreutzfeld
- University of California, San Francisco, San Francisco, California, USA
| | | | - Martin Okitwi
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Stephen Orena
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - Thomas Katairo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Melissa D. Conrad
- University of California, San Francisco, San Francisco, California, USA
| | | | - Jennifer Legac
- University of California, San Francisco, San Francisco, California, USA
| | - Ozkan Aydemir
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | - Barbara Forte
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Peter Campbell
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Alasdair Smith
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Hiroki Kano
- Mitsubishi Tanabe Pharma Corporation, Yokohama, Japan
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13
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Xu H. The slow but steady rise of binding free energy calculations in drug discovery. J Comput Aided Mol Des 2023; 37:67-74. [PMID: 36469232 DOI: 10.1007/s10822-022-00494-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Binding free energy calculations are increasingly used in drug discovery research to predict protein-ligand binding affinities and to prioritize candidate drug molecules accordingly. It has taken decades of collective effort to transform this academic concept into a technology adopted by the pharmaceutical and biotech industry. Having personally witnessed and taken part in this transformation, here I recount the (incomplete) list of problems that had to be solved to make this computational tool practical and suggest areas of future development.
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Affiliation(s)
- Huafeng Xu
- Roivant Discovery, 151 West 42nd Street, New York, NY, 10036, USA.
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14
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A facile and efficient synthesis of highly functionalized pyrroles via a four-component one-pot reaction in the presence of Ni(II) Schiff base/SBA-15 heterogeneous catalyst. RESEARCH ON CHEMICAL INTERMEDIATES 2023. [DOI: 10.1007/s11164-023-04953-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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15
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Dhawale S, Pandit M, Thete K, Ighe D, Gawale S, Bhosle P, Lokwani DK. In silico approach towards polyphenols as targeting glucosamine-6-phosphate synthase for Candida albicans. J Biomol Struct Dyn 2023; 41:12038-12054. [PMID: 36629053 DOI: 10.1080/07391102.2022.2164797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/27/2022] [Indexed: 01/12/2023]
Abstract
Candida albicans is one of the most common species of fungus with life-threatening systemic infections and a high mortality rate. The outer cell wall layer of C. albicans is packed with mannoproteins and glycosylated polysaccharide moieties that play an essential role in the interaction with host cells and tissues. The glucosamine-6-phosphate synthase enzyme produces N-acetylglucosamine, which is a crucial chemical component of the cell wall of Candida albicans. Collectively, these components are essential to maintain the cell shape and for infection. So, its disruption can have serious effects on cell growth and morphology, resulting in cell death. Hence, it is considered a good antifungal target. In this study, we have performed an in silico approach to analyze the inhibitory potential of some polyphenols obtained from plants. Those can be considered important in targeting against the enzyme glucosamine-6-phosphate synthase (PDB-2VF5). The results of the study revealed that the binding affinity of complexes theaflavin and 3-o-malonylglucoside have significant docking scores and binding free energy followed by significant ADMET parameters that predict the drug-likeness property and toxicity of polyphenols as potential ligands. A molecular dynamic simulation was used to test the validity of the docking scores, and it showed that the complex remained stable during the period of the simulation, which ranged from 0 to 100 ns. Theaflavins and 3-o-malonylglucoside may be effective against Candida albicans using a computer-aided drug design methodology that will further enable researchers for future in vitro and in vivo studies, according to our in silico study.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sachin Dhawale
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical education and research, Aurangabad, Maharashtra, India
| | - Madhuri Pandit
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical education and research, Aurangabad, Maharashtra, India
| | - Kanchan Thete
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical education and research, Aurangabad, Maharashtra, India
| | - Dnyaneshwari Ighe
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical education and research, Aurangabad, Maharashtra, India
| | - Sachin Gawale
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical education and research, Aurangabad, Maharashtra, India
| | - Pallavi Bhosle
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical education and research, Aurangabad, Maharashtra, India
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16
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Maclean AE, Hayward JA, Huet D, van Dooren GG, Sheiner L. The mystery of massive mitochondrial complexes: the apicomplexan respiratory chain. Trends Parasitol 2022; 38:1041-1052. [PMID: 36302692 PMCID: PMC10434753 DOI: 10.1016/j.pt.2022.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022]
Abstract
The mitochondrial respiratory chain is an essential pathway in most studied eukaryotes due to its roles in respiration and other pathways that depend on mitochondrial membrane potential. Apicomplexans are unicellular eukaryotes whose members have an impact on global health. The respiratory chain is a drug target for some members of this group, notably the malaria-causing Plasmodium spp. This has motivated studies of the respiratory chain in apicomplexan parasites, primarily Toxoplasma gondii and Plasmodium spp. for which experimental tools are most advanced. Studies of the respiratory complexes in these organisms revealed numerous novel features, including expansion of complex size. The divergence of apicomplexan mitochondria from commonly studied models highlights the diversity of mitochondrial form and function across eukaryotic life.
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Affiliation(s)
- Andrew E Maclean
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Jenni A Hayward
- Research School of Biology, Australian National University, Canberra, Australia
| | - Diego Huet
- Center for Tropical & Emerging Diseases, University of Georgia, Athens, GA, USA; Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, USA
| | - Giel G van Dooren
- Research School of Biology, Australian National University, Canberra, Australia
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK.
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17
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Roseoflavin, a Natural Riboflavin Analogue, Possesses In Vitro and In Vivo Antiplasmodial Activity. Antimicrob Agents Chemother 2022; 66:e0054022. [PMID: 36094195 PMCID: PMC9578400 DOI: 10.1128/aac.00540-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of the human malaria parasite Plasmodium falciparum to access and utilize vital nutrients is critical to its growth and proliferation. Molecules that interfere with these processes could potentially serve as antimalarials. We found that two riboflavin analogues, roseoflavin and 8-aminoriboflavin, inhibit malaria parasite proliferation by targeting riboflavin metabolism and/or the utilization of the riboflavin metabolites flavin mononucleotide and flavin adenine dinucleotide. An additional eight riboflavin analogues were evaluated, but none were found to be more potent than roseoflavin, nor was their activity on target. Focusing on roseoflavin, we tested its antimalarial activity in vivo against Plasmodium vinckei vinckei in mice. We found that roseoflavin decreased the parasitemia by 46-fold following a 4 day suppression test and, on average, increased the survival of mice by 4 to 5 days. Our data are consistent with riboflavin metabolism and/or the utilization of riboflavin-derived cofactors being viable drug targets for the development of new antimalarials and that roseoflavin could serve as a potential starting point.
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18
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Koumpoura C, Nguyen M, Bijani C, Vendier L, Salina EG, Buroni S, Degiacomi G, Cojean S, Loiseau PM, Benoit-Vical F, García-Sosa AT, Baltas M. Design of Anti-infectious Agents from Lawsone in a Three-Component Reaction with Aldehydes and Isocyanides. ACS OMEGA 2022; 7:35635-35655. [PMID: 36249398 PMCID: PMC9558256 DOI: 10.1021/acsomega.2c03421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
The first effective synthetic approach to naphthofuroquinones via a reaction involving lawsone, various aldehydes, and three isocyanides under microwave irradiation afforded derivatives in moderate to good yields. In addition, for less-reactive aldehydes, two naphtho-enaminodione quinones were obtained for the first time, as result of condensation between lawsone and isocyanides. X-ray structure determination for 9 and 2D-NMR spectra of 28 confirmed the obtained structures. All compounds were evaluated for their anti-infectious activities against Plasmodium falciparum, Leishmania donovani, and Mycobacterium tuberculosis. Among the naphthofuroquinone series, 17 exhibited comparatively the best activity against P. falciparum (IC50 = 2.5 μM) and M. tuberculosis (MIC = 9 μM) with better (P. falciparum) or equivalent (M. tuberculosis) values to already-known naphthofuroquinone compounds. Among the two naphtho-enaminodione quinones, 28 exhibited a moderate activity against P. falciparum with a good selectivity index (SI > 36) while also a very high potency against L. donovani (IC50 = 3.5 μM and SI > 28), rendering it very competitive to the reference drug miltefosine. All compounds were studied through molecular modeling on their potential targets for P. falciparum, Pfbc1, and PfDHODH, where 17 showed the most favorable interactions.
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Affiliation(s)
- Christina
L. Koumpoura
- Laboratoire
de Chimie de Coordination du CNRS−UPR8241, Inserm ERL 1289
Team “New antiplasmodial molecules and pharmacological approaches”, 205 route de Narbonne, BP 44099, Toulouse Cedex 31077, France
| | - Michel Nguyen
- Laboratoire
de Chimie de Coordination du CNRS−UPR8241, Inserm ERL 1289
Team “New antiplasmodial molecules and pharmacological approaches”, 205 route de Narbonne, BP 44099, Toulouse Cedex 31077, France
| | - Christian Bijani
- Laboratoire
de Chimie de Coordination du CNRS−UPR8241, Inserm ERL 1289
Team “New antiplasmodial molecules and pharmacological approaches”, 205 route de Narbonne, BP 44099, Toulouse Cedex 31077, France
| | - Laure Vendier
- Laboratoire
de Chimie de Coordination du CNRS−UPR8241, Inserm ERL 1289
Team “New antiplasmodial molecules and pharmacological approaches”, 205 route de Narbonne, BP 44099, Toulouse Cedex 31077, France
| | - Elena G. Salina
- Bach
Institute of Biochemistry, Research Center
of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Silvia Buroni
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Giulia Degiacomi
- Department
of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Sandrine Cojean
- Antiparasite
Chemotherapy, UMR 8076 CNRS BioCIS, Faculty of Pharmacy, University
Paris-Saclay, Châtenay-Malabry 92290, France
| | - Philippe M. Loiseau
- Antiparasite
Chemotherapy, UMR 8076 CNRS BioCIS, Faculty of Pharmacy, University
Paris-Saclay, Châtenay-Malabry 92290, France
| | - Françoise Benoit-Vical
- Laboratoire
de Chimie de Coordination du CNRS−UPR8241, Inserm ERL 1289
Team “New antiplasmodial molecules and pharmacological approaches”, 205 route de Narbonne, BP 44099, Toulouse Cedex 31077, France
| | - Alfonso T. García-Sosa
- Department
of Molecular Technology, Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
| | - Michel Baltas
- Laboratoire
de Chimie de Coordination du CNRS−UPR8241, Inserm ERL 1289
Team “New antiplasmodial molecules and pharmacological approaches”, 205 route de Narbonne, BP 44099, Toulouse Cedex 31077, France
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19
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Pontikos MA, Leija C, Zhao Z, Wang X, Kilgore J, Tornesi B, Adenmatten N, Phillips MA, Williams NS. Development of a biomarker to monitor target engagement after treatment with dihydroorotate dehydrogenase inhibitors. Biochem Pharmacol 2022; 204:115237. [PMID: 36055381 PMCID: PMC9547971 DOI: 10.1016/j.bcp.2022.115237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/22/2022]
Abstract
Dihydroorotate dehydrogenase (DHODH) catalyzes a key step in pyrimidine biosynthesis and has recently been validated as a therapeutic target for malaria through clinical studies on the triazolopyrimidine-based Plasmodium DHODH inhibitor DSM265. Selective toxicity towards Plasmodium species could be achieved because malaria parasites lack pyrimidine salvage pathways, and DSM265 selectively inhibits Plasmodium DHODH over the human enzyme. However, while DSM265 does not inhibit human DHODH, it inhibits DHODH from several preclinical species, including mice, suggesting that toxicity could result from on-target DHODH inhibition in those species. We describe here the use of dihydroorotate (DHO) as a biomarker of DHODH inhibition. Treatment of mammalian cells with DSM265 or the mammalian DHODH inhibitor teriflunomide led to increases in DHO where the extent of biomarker buildup correlated with both dose and inhibitor potency on DHODH. Treatment of mice with leflunomide (teriflunomide prodrug) caused a large dose-dependent buildup of DHO in blood (up to 16-fold) and urine (up to 5,400-fold) that was not observed for mice treated with DSM265. Unbound plasma teriflunomide levels reached 20-85-fold above the mouse DHODH IC50, while free DSM265 levels were only 1.6-4.2-fold above, barely achieving ∼ IC90 concentrations, suggesting that unbound DSM265 plasma levels are not sufficient to block the pathway in vivo. Thus, any toxicity associated with DSM265 treatment in mice is likely caused by off-target mechanisms. The identification of a robust biomarker for mammalian DHODH inhibition represents an important advance to generally monitor for on-target effects in preclinical and clinical applications of DHODH inhibitors used to treat human disease.
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Affiliation(s)
- Michael A Pontikos
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390-9135, United States
| | - Christopher Leija
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390-9135, United States
| | - Zhiyu Zhao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390, United States
| | - Xiaoyu Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390-9135, United States
| | - Jessica Kilgore
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390-9135, United States
| | - Belen Tornesi
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390-9135, United States.
| | - Noelle S Williams
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390-9135, United States.
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20
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Janin YL. On drug discovery against infectious diseases and academic medicinal chemistry contributions. Beilstein J Org Chem 2022; 18:1355-1378. [PMID: 36247982 PMCID: PMC9531561 DOI: 10.3762/bjoc.18.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/21/2022] [Indexed: 11/23/2022] Open
Abstract
This perspective is an attempt to document the problems that medicinal chemists are facing in drug discovery. It is also trying to identify relevant/possible, research areas in which academics can have an impact and should thus be the subject of grant calls. Accordingly, it describes how hit discovery happens, how compounds to be screened are selected from available chemicals and the possible reasons for the recurrent paucity of useful/exploitable results reported. This is followed by the successful hit to lead stories leading to recent and original antibacterials which are, or about to be, used in human medicine. Then, illustrated considerations and suggestions are made on the possible inputs of academic medicinal chemists. This starts with the observation that discovering a “good” hit in the course of a screening campaign still rely on a lot of luck – which is within the reach of academics –, that the hit to lead process requires a lot of chemistry and that if public–private partnerships can be important throughout these stages, they are absolute requirements for clinical trials. Concerning suggestions to improve the current hit success rate, one academic input in organic chemistry would be to identify new and pertinent chemical space, design synthetic accesses to reach these and prepare the corresponding chemical libraries. Concerning hit to lead programs on a given target, if no new hits are available, previously reported leads along with new structural data can be pertinent starting points to design, prepare and assay original analogues. In conclusion, this text is an actual plea illustrating that, in many countries, academic research in medicinal chemistry should be more funded, especially in the therapeutic area neglected by the industry. At the least, such funds would provide the intensive to secure series of hopefully relevant chemical entities which appears to often lack when considering the results of academic as well as industrial screening campaigns.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
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21
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Identification of novel Plasmodium falciparum dihydroorotate dehydrogenase inhibitors for malaria using in silico studies. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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