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Pires PM, Santos D, Calisto F, Pereira M. The monotopic quinone reductases from Staphylococcus aureus. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149488. [PMID: 38950690 DOI: 10.1016/j.bbabio.2024.149488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/27/2024] [Indexed: 07/03/2024]
Abstract
Staphylococcus aureus, a Gram-positive bacterium, is an opportunistic pathogen and one of the most frequent causes for community acquired and nosocomial infections that has become a major public health threat due to the increased incidence of its drug resistance. Although being a prominent pathogen, its energetic metabolism is still underexplored, and its respiratory enzymes have been escaping attention. S. aureus can adapt to different environmental conditions by performing both aerobic and anaerobic respirations, which is particularly important as it frequently colonizes niches with different oxygen concentrations. This adaptability is derived from the composition of its respiratory chain, specifically from the presence of terminal electron acceptor reductases. The plasticity of S. aureus energy metabolism is enlarged by the ten quinone reductases encoded in its genome, eight of them being monotopic proteins. The role of these proteins is critical as they connect the different catabolic pathways to the respiratory chain. In this work, we identify, describe, and revise the monotopic quinone reductases present in S. aureus, providing an integrated view of its respiratory chain.
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Affiliation(s)
- Patrícia M Pires
- University of Lisbon, Faculty of Sciences, Department of Chemistry and Biochemistry and BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - David Santos
- University of Lisbon, Faculty of Sciences, Department of Chemistry and Biochemistry and BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Filipa Calisto
- University of Lisbon, Faculty of Sciences, Department of Chemistry and Biochemistry and BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Manuela Pereira
- University of Lisbon, Faculty of Sciences, Department of Chemistry and Biochemistry and BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal.
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2
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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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Jones J, Clark RD, Lawless MS, Miller DW, Waldman M. The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations. J Comput Aided Mol Des 2024; 38:14. [PMID: 38499823 DOI: 10.1007/s10822-024-00552-6] [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: 08/16/2023] [Accepted: 02/13/2024] [Indexed: 03/20/2024]
Abstract
Computer-aided drug design has advanced rapidly in recent years, and multiple instances of in silico designed molecules advancing to the clinic have demonstrated the contribution of this field to medicine. Properly designed and implemented platforms can drastically reduce drug development timelines and costs. While such efforts were initially focused primarily on target affinity/activity, it is now appreciated that other parameters are equally important in the successful development of a drug and its progression to the clinic, including pharmacokinetic properties as well as absorption, distribution, metabolic, excretion and toxicological (ADMET) properties. In the last decade, several programs have been developed that incorporate these properties into the drug design and optimization process and to varying degrees, allowing for multi-parameter optimization. Here, we introduce the Artificial Intelligence-driven Drug Design (AIDD) platform, which automates the drug design process by integrating high-throughput physiologically-based pharmacokinetic simulations (powered by GastroPlus) and ADMET predictions (powered by ADMET Predictor) with an advanced evolutionary algorithm that is quite different than current generative models. AIDD uses these and other estimates in iteratively performing multi-objective optimizations to produce novel molecules that are active and lead-like. Here we describe the AIDD workflow and details of the methodologies involved therein. We use a dataset of triazolopyrimidine inhibitors of the dihydroorotate dehydrogenase from Plasmodium falciparum to illustrate how AIDD generates novel sets of molecules.
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Affiliation(s)
- Jeremy Jones
- Simulations Plus, Inc., 42505 10th Street West, Lancaster, CA, 93534‑7059, USA.
| | - Robert D Clark
- The Indiana University Luddy School of Informatics, Computing and Engineering, 700 N. Woodlawn Avenue, Bloomington, IN, 47408, USA
| | - Michael S Lawless
- Simulations Plus, Inc., 42505 10th Street West, Lancaster, CA, 93534‑7059, USA
| | - David W Miller
- Simulations Plus, Inc., 42505 10th Street West, Lancaster, CA, 93534‑7059, USA
| | - Marvin Waldman
- Simulations Plus, Inc., 42505 10th Street West, Lancaster, CA, 93534‑7059, USA
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4
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Lima Costa AH, Bezerra KS, de Lima Neto JX, Oliveira JIN, Galvão DS, Fulco UL. Deciphering Interactions between Potential Inhibitors and the Plasmodium falciparum DHODH Enzyme: A Computational Perspective. J Phys Chem B 2023; 127:9461-9475. [PMID: 37897437 DOI: 10.1021/acs.jpcb.3c05738] [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: 10/30/2023]
Abstract
Malaria is a parasitic disease that, in its most severe form, can even lead to death. Insect-resistant vectors, insufficiently effective vaccines, and drugs that cannot stop parasitic infestations are making the fight against the disease increasingly difficult. It is known that the enzyme dihydroorotate dehydrogenase (DHODH) is of paramount importance for the synthesis of pyrimidine from the Plasmodium precursor, that is, for its growth and reproduction. Therefore, its blockade can lead to disruption of the parasite's life cycle in the vertebrate host. In this scenario, PfDHODH inhibitors have been considered candidates for a new therapy to stop the parasitic energy source. Given what is known, in this work, we applied molecular fractionation with conjugated caps (MFCC) in the framework of the quantum formalism of density functional theory (DFT) to evaluate the energies of the interactions between the enzyme and the different triazolopyrimidines (DSM483, DMS557, and DSM1), including a complex carrying the mutation C276F. From these results, it was possible to identify the main features of each system, focusing on the wild-type and mutant PfDHODH and examining the major amino acid residues that are part of the four complexes. Our analysis provides new information that can be used to develop new drugs that could prove to be more effective alternatives to present antimalarial drugs.
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Affiliation(s)
- Aranthya Hevelly Lima Costa
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - Katyanna Sales Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
- Applied Physics Department, University of Campinas, 130838-59 Campinas, São Paulo, Brazil
| | - José Xavier de Lima Neto
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - Jonas Ivan Nobre Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - Douglas Soares Galvão
- Applied Physics Department, University of Campinas, 130838-59 Campinas, São Paulo, Brazil
| | - Umberto Laino Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
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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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Elamin EM, Eshage SE, Mohmmode SM, Mukhtar RM, Mahjoub M, Sadelin E, Shoaib TH, Edris A, Elshamly EM, Makki AA, Ashour A, Sherif AE, Osman W, Ibrahim SRM, Mohamed GA, Alzain AA. Discovery of dual-target natural antimalarial agents against DHODH and PMT of Plasmodium falciparum: pharmacophore modelling, molecular docking, quantum mechanics, and molecular dynamics simulations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023; 34:709-728. [PMID: 37665563 DOI: 10.1080/1062936x.2023.2251876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023]
Abstract
Malaria is a lethal disease that claims thousands of lives worldwide annually. The objective of this study was to identify new natural compounds that can target two P. falciparum enzymes; P. falciparum Dihydroorotate dehydrogenase (PfDHODH) and P. falciparum phosphoethanolamine methyltransferase (PfPMT). To accomplish this, e-pharmacophore modelling and molecular docking were employed against PfDHODH. Following this, 1201 natural compounds with docking scores of ≤ -7 kcal/mol were docked into the active site of the second enzyme PMT. The top nine compounds were subjected to further investigation using MM-GBSA free binding energy calculations and ADME analysis. The results revealed favourable free binding energy values better than the references, as well as acceptable pharmacokinetic properties. Compounds ZINC000013377887, ZINC000015113777, and ZINC000085595753 were scrutinized to assess their interaction stability with the PfDHODH enzyme, and chemical stability reactivity using molecular dynamics (MD) simulation and density functional theory (DFT) calculations. These findings indicate that the three natural compounds are potential candidates for dual PfDHODH and PfPMT inhibitors for malaria treatment.
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Affiliation(s)
- E M Elamin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - S E Eshage
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - S M Mohmmode
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - R M Mukhtar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - M Mahjoub
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - E Sadelin
- Department of Pharmaceutics, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - T H Shoaib
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - A Edris
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - E M Elshamly
- Department of Molecular Biotechnology, Hochschule Anhalt, Köthen, Germany
| | - A A Makki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - A Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, AlKharj, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Al Mansurah, Egypt
| | - A E Sherif
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, AlKharj, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Al Mansurah, Egypt
| | - W Osman
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, AlKharj, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
| | - S R M Ibrahim
- Preparatory Year Program, Department of Chemistry, Batterjee Medical College, Jeddah, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - G A Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - A A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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7
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Sousa FM, Pires P, Barreto A, Refojo PN, Silva MS, Fernandes PB, Carapeto AP, Robalo TT, Rodrigues MS, Pinho MG, Cabrita EJ, Pereira MM. Unveiling the membrane bound dihydroorotate: Quinone oxidoreductase from Staphylococcus aureus. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148948. [PMID: 36481274 DOI: 10.1016/j.bbabio.2022.148948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Staphylococcus aureus is an opportunistic pathogen and one of the most frequent causes for community acquired and nosocomial bacterial infections. Even so, its energy metabolism is still under explored and its respiratory enzymes have been vastly overlooked. In this work, we unveil the dihydroorotate:quinone oxidoreductase (DHOQO) from S. aureus, the first example of a DHOQO from a Gram-positive organism. This protein was shown to be a FMN containing menaquinone reducing enzyme, presenting a Michaelis-Menten behaviour towards the two substrates, which was inhibited by Brequinar, Leflunomide, Lapachol, HQNO, Atovaquone and TFFA with different degrees of effectiveness. Deletion of the DHOQO coding gene (Δdhoqo) led to lower bacterial growth rates, and effected in cell morphology and metabolism, most importantly in the pyrimidine biosynthesis, here systematized for S. aureus MW2 for the first time. This work unveils the existence of a functional DHOQO in the respiratory chain of the pathogenic bacterium S. aureus, enlarging the understanding of its energy metabolism.
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Affiliation(s)
- Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Patrícia Pires
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Andreia Barreto
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Micael S Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro B Fernandes
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Ana P Carapeto
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Tiago T Robalo
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mário S Rodrigues
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mariana G Pinho
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Eurico J Cabrita
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal.
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8
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Sarma M, Abdalla M, Zothantluanga JH, Abdullah Thagfan F, Umar AK, Chetia D, Almanaa TN, Al-Shouli ST. Multi-target molecular dynamic simulations reveal glutathione-S-transferase as the most favorable drug target of knipholone in Plasmodium falciparum. J Biomol Struct Dyn 2023; 41:12808-12824. [PMID: 36752355 DOI: 10.1080/07391102.2023.2175378] [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: 10/12/2022] [Accepted: 01/07/2023] [Indexed: 02/09/2023]
Abstract
Knipholone is an antiplasmodial phytocompound obtained from the roots of Kniphofia foliosa. Despite several available studies, the molecular drug targets of knipholone in P. falciparum remained unknown. Nowadays, in silico techniques are widely used to study the molecular interactions between compounds and proteins as they provide results quickly with high precision and accuracy. In this study, we aim to identify the potential molecular drug targets of knipholone in P. falciparum. We selected 10 proteins of P. falciparum with unique metabolic functions and we found that knipholone showed better binding affinity than the native ligands of 6 proteins. Out of the 6 proteins, knipholone showed better enzyme inhibitory potential than the native ligands of 4 proteins. We carried out a 100 ns MD simulations for knipholone and the native ligands of four proteins and this was followed by binding free energy calculations. In each step, the performance of knipholone was compared to the native ligands of the proteins. Knipholone outperformed the native ligand of Glutathione-S-Transferase (1OKT) at crucial computational studies as evidence from the lower protein-ligand root mean square deviation value, protein root mean square fluctuation value, and protein-ligand binding free energies. The ligand properties of knipholone provide additional evidence for its stability and it maintains adequate protein-ligand contacts during the entire simulation. The density functional theory study also supported the stability of knipholone at the active binding site of 1OKT. From the studied proteins, we conclude that Glutathione-S-Transferase is the most favorable drug target for knipholone in P. falciparum.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Malita Sarma
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, China
| | - James H Zothantluanga
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Felwa Abdullah Thagfan
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Abd Kakhar Umar
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Indonesia
| | - Dipak Chetia
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Samia T Al-Shouli
- Immunology Unit, Pathology department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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Russo TA, Umland TC, Deng X, El Mazouni F, Kokkonda S, Olson R, Carlino-MacDonald U, Beanan J, Alvarado CL, Tomchick DR, Hutson A, Chen H, Posner B, Rathod PK, Charman SA, Phillips MA. Repurposed dihydroorotate dehydrogenase inhibitors with efficacy against drug-resistant Acinetobacter baumannii. Proc Natl Acad Sci U S A 2022; 119:e2213116119. [PMID: 36512492 PMCID: PMC9907071 DOI: 10.1073/pnas.2213116119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022] Open
Abstract
New antimicrobials are needed for the treatment of extensively drug-resistant Acinetobacter baumannii. The de novo pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) is a validated drug target for malaria and human autoimmune diseases. We provide genetic evidence that A. baumannii DHODH (AbDHODH) is essential for bacterial survival in rodent infection models. We chemically validate the target by repurposing a unique library of ~450 triazolopyrimidine/imidazopyrimidine analogs developed for our malaria DHODH program to identify 21 compounds with submicromolar activity on AbDHODH. The most potent (DSM186, DHODH IC50 28 nM) had a minimal inhibitory concentration of ≤1 µg/ml against geographically diverse A. baumannii strains, including meropenem-resistant isolates. A structurally related analog (DSM161) with a long in vivo half-life conferred significant protection in the neutropenic mouse thigh infection model. Encouragingly, the development of resistance to these compounds was not identified in vitro or in vivo. Lastly, the X-ray structure of AbDHODH bound to DSM186 was solved to 1.4 Å resolution. These data support the potential of AbDHODH as a drug target for the development of antimicrobials for the treatment of A. baumannii and potentially other high-risk bacterial infections.
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Affiliation(s)
- Thomas A. Russo
- Department of Medicine, Veterans Administration Western New York Healthcare System, Buffalo, NY14215
- The Department of Medicine, University at Buffalo-State University of New York, Buffalo, NY14203
- Department of Microbiology and Immunology, University at Buffalo-State University of New York, Buffalo, NY14203
- The Witebsky Center for Microbial Pathogenesis, University at Buffalo-State University of New York, Buffalo, NY14203
| | - Timothy C. Umland
- Department of Structural Biology, University at Buffalo State University of New York, Buffalo, NY14203
- Hauptman Woodward Medical Research Institute, Buffalo, NY14203
| | - Xiaoyi Deng
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX75390
| | - Farah El Mazouni
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX75390
| | - Sreekanth Kokkonda
- Department of Chemistry, University of Washington, Seattle, WA98195
- Department of Global Health, University of Washington, Seattle, WA98195
| | - Ruth Olson
- Department of Medicine, Veterans Administration Western New York Healthcare System, Buffalo, NY14215
- The Department of Medicine, University at Buffalo-State University of New York, Buffalo, NY14203
| | - Ulrike Carlino-MacDonald
- Department of Medicine, Veterans Administration Western New York Healthcare System, Buffalo, NY14215
- The Department of Medicine, University at Buffalo-State University of New York, Buffalo, NY14203
| | - Janet Beanan
- Department of Medicine, Veterans Administration Western New York Healthcare System, Buffalo, NY14215
- The Department of Medicine, University at Buffalo-State University of New York, Buffalo, NY14203
| | - Cassandra L. Alvarado
- Department of Medicine, Veterans Administration Western New York Healthcare System, Buffalo, NY14215
- The Department of Medicine, University at Buffalo-State University of New York, Buffalo, NY14203
| | - Diana R. Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, TX75390
| | - Alan Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY14203
| | - Hong Chen
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX75390
| | - Bruce Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX75390
| | - Pradipsinh K. Rathod
- Department of Chemistry, University of Washington, Seattle, WA98195
- Department of Global Health, University of Washington, Seattle, WA98195
| | - Susan A. Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC3052Australia
| | - Margaret A. Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX75390
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Vyas VK, Shukla T, Tulsian K, Sharma M, Patel S. Integrated structure-guided computational design of novel substituted quinolizin-4-ones as Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors. Comput Biol Chem 2022; 101:107787. [DOI: 10.1016/j.compbiolchem.2022.107787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 11/03/2022] [Accepted: 11/06/2022] [Indexed: 11/09/2022]
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11
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Ibrahim ZY, Uzairu A, Shallangwa GA, Abechi SE. Pharmacokinetic predictions and docking studies of substituted aryl amine-based triazolopyrimidine designed inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH). FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021. [DOI: 10.1186/s43094-021-00288-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The sixteen (16) designed data set of substituted aryl amine-based triazolopyrimidine were docked against Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) employing Molegro Virtual Docker (MVD) software and their pharmacokinetic property determined through SwissADME predictor.
Results
The docking studies shows compound D16, 5-((6-methoxy-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)amino)benzo[b]thiophen-4-ol to be the most interactive and stable derivative (re-rank score = − 114.205 kcal/mol) resulting from the hydrophobic as well as hydrogen interactions. The hydrogen interaction produced one hydrogen bond with the active residues LEU359 (H∙∙H∙∙O) at a bond distances of 2.2874 Å. All the designed derivatives were found to pass the Lipinski rule of five tests, supporting the drug-likeliness of the designed compounds.
Conclusion
The ADME analysis revealed a perfect concurrence with the Lipinski Ro5, where the derivatives were found to possess good pharmacokinetic properties such as molar refractivity (MR), number of rotatable bonds (nRotb), log of skin permeability (log Kp), blood-brain barrier (BBB). These results could a deciding factor for the optimization of novel antimalarial compounds.
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12
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Palmer MJ, Deng X, Watts S, Krilov G, Gerasyuto A, Kokkonda S, El Mazouni F, White J, White KL, Striepen J, Bath J, Schindler KA, Yeo T, Shackleford DM, Mok S, Deni I, Lawong A, Huang A, Chen G, Wang W, Jayaseelan J, Katneni K, Patil R, Saunders J, Shahi SP, Chittimalla R, Angulo-Barturen I, Jiménez-Díaz MB, Wittlin S, Tumwebaze PK, Rosenthal PJ, Cooper RA, Aguiar ACC, Guido RVC, Pereira DB, Mittal N, Winzeler EA, Tomchick DR, Laleu B, Burrows JN, Rathod PK, Fidock DA, Charman SA, Phillips MA. Potent Antimalarials with Development Potential Identified by Structure-Guided Computational Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series. J Med Chem 2021; 64:6085-6136. [PMID: 33876936 DOI: 10.1021/acs.jmedchem.1c00173] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dihydroorotate dehydrogenase (DHODH) has been clinically validated as a target for the development of new antimalarials. Experience with clinical candidate triazolopyrimidine DSM265 (1) suggested that DHODH inhibitors have great potential for use in prophylaxis, which represents an unmet need in the malaria drug discovery portfolio for endemic countries, particularly in areas of high transmission in Africa. We describe a structure-based computationally driven lead optimization program of a pyrrole-based series of DHODH inhibitors, leading to the discovery of two candidates for potential advancement to preclinical development. These compounds have improved physicochemical properties over prior series frontrunners and they show no time-dependent CYP inhibition, characteristic of earlier compounds. Frontrunners have potent antimalarial activity in vitro against blood and liver schizont stages and show good efficacy in Plasmodium falciparum SCID mouse models. They are equally active against P. falciparum and Plasmodium vivax field isolates and are selective for Plasmodium DHODHs versus mammalian enzymes.
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Affiliation(s)
| | - Xiaoyi Deng
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Shawn Watts
- Schrodinger, Inc., 120 West 45th St, 17th Floor, New York, New York 100036-4041, United States
| | - Goran Krilov
- Schrodinger, Inc., 120 West 45th St, 17th Floor, New York, New York 100036-4041, United States
| | - Aleksey Gerasyuto
- Schrodinger, Inc., 120 West 45th St, 17th Floor, New York, New York 100036-4041, United States
| | - Sreekanth Kokkonda
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Farah El Mazouni
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - John White
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Karen L White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Josefine Striepen
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Jade Bath
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Kyra A Schindler
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - David M Shackleford
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Ioanna Deni
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Aloysus Lawong
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Ann Huang
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Wen Wang
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Jaya Jayaseelan
- 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
| | - Rahul Patil
- 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
| | | | | | - Iñigo Angulo-Barturen
- TAD, Biscay Science and Technology Park, Astondo Bidea, BIC Bizkaia Bd 612, Derio, 48160 Bizkaia, Basque Country, Spain
| | - María Belén Jiménez-Díaz
- TAD, Biscay Science and Technology Park, Astondo Bidea, BIC Bizkaia Bd 612, Derio, 48160 Bizkaia, Basque Country, Spain
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | | | - Philip J Rosenthal
- Department of Medicine, University of California, San Francisco, California 94143, United States
| | - Roland A Cooper
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California 94901, United States
| | | | - Rafael V C Guido
- University of Sao Paulo, Sao Carlos Institute of Physics, Sáo Carlos, SP 13560-970, Brazil
| | - Dhelio B Pereira
- Tropical Medicine Research Center of Rondonia, Av. Guaporé, 215, Porto Velho, RO 76812-329, Brazil
| | - Nimisha Mittal
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, School of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Elizabeth A Winzeler
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, School of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Diana R Tomchick
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Benoît Laleu
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | - Pradipsinh K Rathod
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States.,Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
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13
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Sato D, Hartuti ED, Inaoka DK, Sakura T, Amalia E, Nagahama M, Yoshioka Y, Tsuji N, Nozaki T, Kita K, Harada S, Matsubayashi M, Shiba T. Structural and Biochemical Features of Eimeria tenella Dihydroorotate Dehydrogenase, a Potential Drug Target. Genes (Basel) 2020; 11:genes11121468. [PMID: 33297567 PMCID: PMC7762340 DOI: 10.3390/genes11121468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/23/2022] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is a mitochondrial monotopic membrane protein that plays an essential role in the pyrimidine de novo biosynthesis and electron transport chain pathways. In Eimeria tenella, an intracellular apicomplexan parasite that causes the most severe form of chicken coccidiosis, the activity of pyrimidine salvage pathway at the intracellular stage is negligible and it relies on the pyrimidine de novo biosynthesis pathway. Therefore, the enzymes of the de novo pathway are considered potential drug target candidates for the design of compounds with activity against this parasite. Although, DHODHs from E. tenella (EtDHODH), Plasmodium falciparum (PfDHODH), and human (HsDHODH) show distinct sensitivities to classical DHODH inhibitors, in this paper, we identify ferulenol as a potent inhibitor of both EtDHODH and HsDHODH. Additionally, we report the crystal structures of EtDHODH and HsDHODH in the absence and presence of ferulenol. Comparison of these enzymes showed that despite similar overall structures, the EtDHODH has a long insertion in the N-terminal helix region that assumes a disordered configuration. In addition, the crystal structures revealed that the ferulenol binding pocket of EtDHODH is larger than that of HsDHODH. These differences can be explored to accelerate structure-based design of inhibitors specifically targeting EtDHODH.
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Affiliation(s)
- Dan Sato
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Endah Dwi Hartuti
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
| | - Daniel Ken Inaoka
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
- Correspondence: (D.K.I.); (T.S.); Tel.: +81-95-819-7230 (D.K.I.); Tel./Fax: +81-75-724-7541 (T.S.)
| | - Takaya Sakura
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
| | - Eri Amalia
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
| | - Madoka Nagahama
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Yukina Yoshioka
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Naotoshi Tsuji
- Department of Parasitology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan;
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
- Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Makoto Matsubayashi
- Division of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku Orai Kita, Izumisano, Osaka 598-8531, Japan;
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
- Correspondence: (D.K.I.); (T.S.); Tel.: +81-95-819-7230 (D.K.I.); Tel./Fax: +81-75-724-7541 (T.S.)
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14
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Driving antimalarial design through understanding of target mechanism. Biochem Soc Trans 2020; 48:2067-2078. [PMID: 32869828 PMCID: PMC7609028 DOI: 10.1042/bst20200224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 11/17/2022]
Abstract
Malaria continues to be a global health threat, affecting approximately 219 million people in 2018 alone. The recurrent development of resistance to existing antimalarials means that the design of new drug candidates must be carefully considered. Understanding of drug target mechanism can dramatically accelerate early-stage target-based development of novel antimalarials and allows for structural modifications even during late-stage preclinical development. Here, we have provided an overview of three promising antimalarial molecular targets, PfDHFR, PfDHODH and PfA-M1, and their associated inhibitors which demonstrate how mechanism can inform drug design and be effectively utilised to generate compounds with potent inhibitory activity.
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15
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Owoloye A, Enejoh OA, Akanbi OM, Bankole OM. Molecular docking analysis of Plasmodium falciparum dihydroorotate dehydrogenase towards the design of effective inhibitors. Bioinformation 2020; 16:672-678. [PMID: 34621112 PMCID: PMC8457017 DOI: 10.6026/97320630016672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/29/2020] [Accepted: 07/31/2020] [Indexed: 11/23/2022] Open
Abstract
Malaria remains a global public health burden with significant mortality and morbidity. Despite the several approved drugs available for its management, the parasite has developed resistance to virtually all known antimalarial drugs. The development of a new drug that can combat resistant to Artemisinin based Combination Therapies (ACTs) for malaria is imperative. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH), a flavin-dependent mitochondrial enzyme is vital in the parasite's pyrimidine biosynthesis is a well-known drug target. Therefore, it is of interest to document the MOLECULAR DOCKING analysis (using Maestro, Schrodinger) data of DIHYDROOROTATE DEHYDROGENASE PfDHODH from P. falciparum towards the design of effective inhibitors. The molecular docking features of 10 compounds with reference to chloroquine with PfDHODH are documented in this report for further consideration.
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Affiliation(s)
- Afolabi Owoloye
- Parasitology Unit, Department of Animal and Environmental Biology, Adekunle Ajasin University, Akungba-Akoko, Nigeria
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Ojochenemi A Enejoh
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Olusegun M Akanbi
- Parasitology Unit, Department of Animal and Environmental Biology, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Owolabi M Bankole
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba-Akoko, Nigeria
- Department of Chemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
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16
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Investigating the amino acid sequences of membrane bound dihydroorotate:quinone oxidoreductases (DHOQOs): Structural and functional implications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148321. [PMID: 32991846 DOI: 10.1016/j.bbabio.2020.148321] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/26/2022]
Abstract
Dihydroorotate:quinone oxidoreductases (DHOQOs) are membrane bound enzymes responsible for oxidizing dihydroorotate (DHO) to orotate with concomitant reduction of quinone to quinol. They have FMN as prosthetic group and are part of the monotopic quinone reductase superfamily. These enzymes are also members of the dihydroorotate dehydrogenases (DHODHs) family, which besides membrane bound DHOQOs, class 2, includes soluble enzymes which reduce either NAD+ or fumarate, class 1. As key enzymes in both the de novo pyrimidine biosynthetic pathway as well as in the energetic metabolism, inhibitors of DHOQOs have been investigated as leads for therapeutics in cancer, immunological disorders and bacterial/viral infections. This work is a thorough bioinformatic approach on the structural conservation and taxonomic distribution of DHOQOs. We explored previously established structural/functional hallmarks of these enzymes, while searching for uncharacterized common elements. We also discuss the cellular role of DHOQOs and organize the identified protein sequences within six sub-classes 2A to 2F, according to their taxonomic origin and sequence traits. We concluded that DHOQOs are present in Archaea, Eukarya and Bacteria, including the first recognition in Gram-positive organisms. DHOQOs can be the single dihydroorotate dehydrogenase encoded in the genome of a species, or they can coexist with other DHODHs, as the NAD+ or fumarate reducing enzymes. Furthermore, we show that the type of catalytic base present in the active site is not an absolute criterium to distinguish between class 1 and class 2 enzymes. We propose the existence of a quinone binding motif ("ExAH") adjacent to a hydrophobic cavity present in the membrane interacting N-terminal domain.
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17
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Pinheiro S, Pinheiro EMC, Muri EMF, Pessôa JC, Cadorini MA, Greco SJ. Biological activities of [1,2,4]triazolo[1,5-a]pyrimidines and analogs. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02609-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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18
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Ibrahim ZY, Uzairu A, Shallangwa G, Abechi S. QSAR and molecular docking based design of some indolyl-3-ethanone-α-thioethers derivatives as Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-2955-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
AbstractMalaria, a disease caused by one of the world’s fatal parasites Plasmodium falciparum, is responsible for over a million death annually. P. falciparum dihydroorotate dehydrogenase (PfDHODH) is a validated target of this deadly parasite. Quantitative structure–activity relationship and molecular docking in silico methods were employed in the discovery of unique PfDHODH inhibitors from the computational design derivatives of indolyl-3-ethanone-α-thioethers through models generation via a genetic function algorithm methods. The best model indicates good power of prediction with coefficient of determination, R2 = 0.9482, adjusted coefficient of determination ($${\text{R}}_{\text{adj}}^{2}$$Radj2) = 0.9288, Leave one out cross-validation coefficient (Q2) = 0.9201 and the external validation ($${\text{R}}_{\text{pred}}^{2}$$Rpred2) = 0.6467. The contribution of every descriptor in the model was investigated through finding their mean effect to (pIC50) the activities of the compounds. With MATS5m (− 0.11725), RDF75m (− 0.12097), VE3_Dzp (0.14697), and MLFER_BH (1.08528) contributing more to the model, while AATSC8p (− 0.04833) and minHBa (0.05430) contributed the least to the model. Hence, the mean effect indicated MLFER_BH to be the most relevant descriptor, which aided the design of five derivatives of indolyl-3-ethanone-α-thioethers. All the designed antimalarial compounds were deeply docked within the binding region thereby forming several hydrogens and hydrophobic bonds leading to the generation of better binding affinity and high binding scores (− 156.181 kcal/mol) compared to the design template (− 138.201 kcal/mol) and the standard drug (− 128.467 kcal/mol). Furthermore, all the five designed antimalarial compounds were found to be better bonded to the binding pocket of PfDHODH than other compounds reported by other researchers.
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19
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Kokkonda S, Deng X, White KL, El Mazouni F, White J, Shackleford DM, Katneni K, Chiu FCK, Barker H, McLaren J, Crighton E, Chen G, Angulo-Barturen I, Jimenez-Diaz MB, Ferrer S, Huertas-Valentin L, Martinez-Martinez MS, Lafuente-Monasterio MJ, Chittimalla R, Shahi SP, Wittlin S, Waterson D, Burrows JN, Matthews D, Tomchick D, Rathod PK, Palmer MJ, Charman SA, Phillips MA. Lead Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series for the Treatment of Malaria. J Med Chem 2020; 63:4929-4956. [PMID: 32248693 DOI: 10.1021/acs.jmedchem.0c00311] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Malaria puts at risk nearly half the world's population and causes high mortality in sub-Saharan Africa, while drug resistance threatens current therapies. The pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) is a validated target for malaria treatment based on our finding that triazolopyrimidine DSM265 (1) showed efficacy in clinical studies. Herein, we describe optimization of a pyrrole-based series identified using a target-based DHODH screen. Compounds with nanomolar potency versus Plasmodium DHODH and Plasmodium parasites were identified with good pharmacological properties. X-ray studies showed that the pyrroles bind an alternative enzyme conformation from 1 leading to improved species selectivity versus mammalian enzymes and equivalent activity on Plasmodium falciparum and Plasmodium vivax DHODH. The best lead DSM502 (37) showed in vivo efficacy at similar levels of blood exposure to 1, although metabolic stability was reduced. Overall, the pyrrole-based DHODH inhibitors provide an attractive alternative scaffold for the development of new antimalarial compounds.
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Affiliation(s)
- Sreekanth Kokkonda
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Xiaoyi Deng
- Departments of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Karen L White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Farah El Mazouni
- Departments of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - John White
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - David M Shackleford
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Francis C K Chiu
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Helena Barker
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Jenna McLaren
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Elly Crighton
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | | | | | - Santiago Ferrer
- GSK, Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | | | | | | | | | | | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | | | | | - Dave Matthews
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Diana Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Pradipsinh K Rathod
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | | | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Margaret A Phillips
- Departments of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
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20
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Aguiar AC, de Sousa LR, Garcia CR, Oliva G, Guido RV. New Molecular Targets and Strategies for Antimalarial Discovery. Curr Med Chem 2019; 26:4380-4402. [DOI: 10.2174/0929867324666170830103003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023]
Abstract
Malaria remains a major health problem, especially because of the emergence
of resistant P. falciparum strains to artemisinin derivatives. In this context, safe and affordable
antimalarial drugs are desperately needed. New proteins have been investigated
as molecular targets for research and development of innovative compounds with welldefined
mechanism of action. In this review, we highlight genetically and clinically validated
plasmodial proteins as drug targets for the next generation of therapeutics. The enzymes
described herein are involved in hemoglobin hydrolysis, the invasion process,
elongation factors for protein synthesis, pyrimidine biosynthesis, post-translational modifications
such as prenylation, phosphorylation and histone acetylation, generation of ATP
in mitochondrial metabolism and aminoacylation of RNAs. Significant advances on proteomics,
genetics, structural biology, computational and biophysical methods provided
invaluable molecular and structural information about these drug targets. Based on this,
several strategies and models have been applied to identify and improve lead compounds.
This review presents the recent progresses in the discovery of antimalarial drug candidates,
highlighting the approaches, challenges, and perspectives to deliver affordable, safe
and low single-dose medicines to treat malaria.
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Affiliation(s)
- Anna Caroline Aguiar
- Sao Carlos Institute of Physics, University of Sao Paulo, PO Box 369, 13560-970, Sao Carlos, SP, Brazil
| | - Lorena R.F. de Sousa
- Sao Carlos Institute of Physics, University of Sao Paulo, PO Box 369, 13560-970, Sao Carlos, SP, Brazil
| | - Celia R.S. Garcia
- Physiology Department, Bioscience Institute, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Glaucius Oliva
- Sao Carlos Institute of Physics, University of Sao Paulo, PO Box 369, 13560-970, Sao Carlos, SP, Brazil
| | - Rafael V.C. Guido
- Sao Carlos Institute of Physics, University of Sao Paulo, PO Box 369, 13560-970, Sao Carlos, SP, Brazil
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21
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Dihydroorotate dehydrogenase inhibitors in anti-infective drug research. Eur J Med Chem 2019; 183:111681. [PMID: 31557612 DOI: 10.1016/j.ejmech.2019.111681] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 08/01/2019] [Accepted: 09/05/2019] [Indexed: 01/08/2023]
Abstract
Pyrimidines are essential for the cell survival and proliferation of living parasitic organisms, such as Helicobacter pylori, Plasmodium falciparum and Schistosoma mansoni, that are able to impact upon human health. Pyrimidine building blocks, in human cells, are synthesised via both de novo biosynthesis and salvage pathways, the latter of which is an effective way of recycling pre-existing nucleotides. As many parasitic organisms lack pyrimidine salvage pathways for pyrimidine nucleotides, blocking de novo biosynthesis is seen as an effective therapeutic means to selectively target the parasite without effecting the human host. Dihydroorotate dehydrogenase (DHODH), which is involved in the de novo biosynthesis of pyrimidines, is a validated target for anti-infective drug research. Recent advances in the DHODH microorganism field are discussed herein, as is the potential for the development of DHODH-targeted therapeutics.
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22
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Garavito MF, Narvaez-Ortiz HY, Pulido DC, Löffler M, Judelson HS, Restrepo S, Zimmermann BH. Phytophthora infestans Dihydroorotate Dehydrogenase Is a Potential Target for Chemical Control - A Comparison With the Enzyme From Solanum tuberosum. Front Microbiol 2019; 10:1479. [PMID: 31316493 PMCID: PMC6611227 DOI: 10.3389/fmicb.2019.01479] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/13/2019] [Indexed: 01/04/2023] Open
Abstract
The oomycete Phytophthora infestans is the causal agent of tomato and potato late blight, a disease that causes tremendous economic losses in the production of solanaceous crops. The similarities between oomycetes and the apicomplexa led us to hypothesize that dihydroorotate dehydrogenase (DHODH), the enzyme catalyzing the fourth step in pyrimidine biosynthetic pathway, and a validated drug target in treatment of malaria, could be a potential target for controlling P. infestans growth. In eukaryotes, class 2 DHODHs are mitochondrially associated ubiquinone-linked enzymes that catalyze the fourth, and only redox step of de novo pyrimidine biosynthesis. We characterized the enzymes from both the pathogen and a host, Solanum tuberosum. Plant DHODHs are known to be class 2 enzymes. Sequence analysis suggested that the pathogen enzyme (PiDHODHs) also belongs to this class. We confirmed the mitochondrial localization of GFP-PiDHODH showing colocalization with mCherry-labeled ATPase in a transgenic pathogen. N-terminally truncated versions of the two DHODHs were overproduced in E. coli, purified, and kinetically characterized. StDHODH exhibited a apparent specific activity of 41 ± 1 μmol min-1 mg-1, a kcatapp of 30 ± 1 s-1, and a Kmapp of 20 ± 1 μM for L-dihydroorotate, and a Kmapp= 30 ± 3 μM for decylubiquinone (Qd). PiDHODH exhibited an apparent specific activity of 104 ± 1 μmol min-1 mg-1, a kcatapp of 75 ± 1 s-1, and a Kmapp of 57 ± 3 μM for L-dihydroorotate, and a Kmapp of 15 ± 1 μM for Qd. The two enzymes exhibited different activities with different quinones and napthoquinone derivatives, and different sensitivities to compounds known to cause inhibition of DHODHs from other organisms. The IC50 for A77 1726, a nanomolar inhibitor of human DHODH, was 2.9 ± 0.6 mM for StDHODH, and 79 ± 1 μM for PiDHODH. In vivo, 0.5 mM A77 1726 decreased mycelial growth by approximately 50%, after 92 h. Collectively, our findings suggest that the PiDHODH could be a target for selective inhibitors and we provide a biochemical background for the development of compounds that could be helpful for the control of the pathogen, opening the way to protein crystallization.
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Affiliation(s)
- Manuel F Garavito
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia.,Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
| | | | - Dania Camila Pulido
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Monika Löffler
- Faculty of Medicine, Department of Biology, University of Marburg, Marburg, Germany
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
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23
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Murphy SC, Duke ER, Shipman KJ, Jensen RL, Fong Y, Ferguson S, Janes HE, Gillespie K, Seilie AM, Hanron AE, Rinn L, Fishbaugher M, VonGoedert T, Fritzen E, Kappe SH, Chang M, Sousa JC, Marcsisin SR, Chalon S, Duparc S, Kerr N, Möhrle JJ, Andenmatten N, Rueckle T, Kublin JG. A Randomized Trial Evaluating the Prophylactic Activity of DSM265 Against Preerythrocytic Plasmodium falciparum Infection During Controlled Human Malarial Infection by Mosquito Bites and Direct Venous Inoculation. J Infect Dis 2019; 217:693-702. [PMID: 29216395 DOI: 10.1093/infdis/jix613] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/29/2017] [Indexed: 11/13/2022] Open
Abstract
Background DSM265 is a selective inhibitor of Plasmodium dihydroorotate dehydrogenase that fully protected against controlled human malarial infection (CHMI) by direct venous inoculation of Plasmodium falciparum sporozoites when administered 1 day before challenge and provided partial protection when administered 7 days before challenge. Methods A double-blinded, randomized, placebo-controlled trial was performed to assess safety, tolerability, pharmacokinetics, and efficacy of 1 oral dose of 400 mg of DSM265 before CHMI. Three cohorts were studied, with DSM265 administered 3 or 7 days before direct venous inoculation of sporozoites or 7 days before 5 bites from infected mosquitoes. Results DSM265-related adverse events consisted of mild-to-moderate headache and gastrointestinal symptoms. DSM265 concentrations were consistent with pharmacokinetic models (mean area under the curve extrapolated to infinity, 1707 µg*h/mL). Placebo-treated participants became positive by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and were treated 7-10 days after CHMI. Among DSM265-treated subjects, 2 of 6 in each cohort were sterilely protected. DSM265-treated recipients had longer times to development of parasitemia than placebo-treated participants (P < .004). Conclusions This was the first CHMI study of a novel antimalarial compound to compare direct venous inoculation of sporozoites and mosquito bites. Times to qRT-PCR positivity and treatment were comparable for both routes. DSM265 given 3 or 7 days before CHMI was safe and well tolerated but sterilely protected only one third of participants.
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Affiliation(s)
- Sean C Murphy
- Department of Laboratory Medicine, University of Washington, Seattle, Washington.,Department of Microbiology, University of Washington, Seattle, Washington.,Center for Emerging and Re-emerging Infectious Diseases, Seattle, Washington.,Seattle Malaria Clinical Trials Center, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Human Challenge Center, Center for Infectious Disease Research, Seattle, Washington
| | - Elizabeth R Duke
- Department of Medicine, University of Washington, Seattle, Washington.,Seattle Malaria Clinical Trials Center, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kelly J Shipman
- Seattle Malaria Clinical Trials Center, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ryan L Jensen
- Seattle Malaria Clinical Trials Center, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Youyi Fong
- Seattle Malaria Clinical Trials Center, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Sue Ferguson
- Seattle Malaria Clinical Trials Center, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Holly E Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kevin Gillespie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Annette M Seilie
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Amelia E Hanron
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Laurie Rinn
- Seattle Malaria Clinical Trials Center, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Matthew Fishbaugher
- Human Challenge Center, Center for Infectious Disease Research, Seattle, Washington
| | - Tracie VonGoedert
- Human Challenge Center, Center for Infectious Disease Research, Seattle, Washington
| | - Emma Fritzen
- Human Challenge Center, Center for Infectious Disease Research, Seattle, Washington
| | - Stefan H Kappe
- Human Challenge Center, Center for Infectious Disease Research, Seattle, Washington
| | - Ming Chang
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Jason C Sousa
- Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | | | | | - Nicola Kerr
- Medicines for Malaria Venture, Geneva, Switzerland
| | | | | | | | - James G Kublin
- Department of Global Health, University of Washington, Seattle, Washington.,Seattle Malaria Clinical Trials Center, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
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24
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Hydroxyazole scaffold-based Plasmodium falciparum dihydroorotate dehydrogenase inhibitors: Synthesis, biological evaluation and X-ray structural studies. Eur J Med Chem 2019; 163:266-280. [DOI: 10.1016/j.ejmech.2018.11.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/16/2018] [Accepted: 11/18/2018] [Indexed: 11/23/2022]
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25
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Triazole derivatives and their antiplasmodial and antimalarial activities. Eur J Med Chem 2019; 166:206-223. [PMID: 30711831 DOI: 10.1016/j.ejmech.2019.01.047] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/19/2019] [Accepted: 01/19/2019] [Indexed: 01/23/2023]
Abstract
Malaria, caused by protozoan parasites of the genus Plasmodium especially by the most prevalent parasite Plasmodium falciparum, represents one of the most devastating and common infectious disease globally. Nearly half of the world population is under the risk of being infected, and more than 200 million new clinical cases with around half a million deaths occur annually. Drug therapy is the mainstay of antimalarial therapy, yet current drugs are threatened by the development of resistance, so it's imperative to develop new antimalarials with great potency against both drug-susceptible and drug-resistant malaria. Triazoles, bearing a five-membered heterocyclic ring with three nitrogen atoms, exhibit promising in vitro antiplasmodial and in vivo antimalarial activities. Moreover, several triazole-based drugs have already used in clinics for the treatment of various diseases, demonstrating the excellent pharmaceutical profiles. Therefore, triazole derivatives have the potential for clinical deployment in the control and eradication of malaria. This review covers the recent advances of triazole derivatives especially triazole hybrids as potential antimalarials. The structure-activity relationship is also discussed to provide an insight for rational designs of more efficient antimalarial candidates.
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26
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Oukoloff K, Lucero B, Francisco KR, Brunden KR, Ballatore C. 1,2,4-Triazolo[1,5-a]pyrimidines in drug design. Eur J Med Chem 2019; 165:332-346. [PMID: 30703745 DOI: 10.1016/j.ejmech.2019.01.027] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 12/01/2022]
Abstract
The 1,2,4-triazolo[1,5-a]pyrimidine (TP) heterocycle, in spite of its relatively simple structure, has proved to be remarkably versatile as evidenced by its use in many different applications reported over the years in different areas of drug design. For example, as the ring system of TPs is isoelectronic with that of purines, this heterocycle has been proposed as a possible surrogate of the purine ring. However, depending on the choice of substituents, the TP ring has also been described as a potentially viable bio-isostere of the carboxylic acid functional group and of the N-acetyl fragment of ε-N-acetylated lysine. In addition, the metal-chelating properties of the TP ring have also been exploited to generate candidate treatments for cancer and parasitic diseases. In the present review article, we discuss recent applications of the TP scaffold in medicinal chemistry, and provide an overview of its properties and methods of synthesis.
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Affiliation(s)
- Killian Oukoloff
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Bobby Lucero
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Karol R Francisco
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Kurt R Brunden
- Center for Neurodegenerative Disease Research, Perelman School of Medicine, University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA, 19104-6323, USA
| | - Carlo Ballatore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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27
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White J, Dhingra SK, Deng X, El Mazouni F, Lee MCS, Afanador GA, Lawong A, Tomchick DR, Ng CL, Bath J, Rathod PK, Fidock DA, Phillips MA. Identification and Mechanistic Understanding of Dihydroorotate Dehydrogenase Point Mutations in Plasmodium falciparum that Confer in Vitro Resistance to the Clinical Candidate DSM265. ACS Infect Dis 2019; 5:90-101. [PMID: 30375858 DOI: 10.1021/acsinfecdis.8b00211] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Malaria is one of the most challenging human infectious diseases, and both prevention and control have been hindered by the development of Plasmodium falciparum resistance to existing therapies. Several new compounds with novel mechanisms are in clinical development for the treatment of malaria, including DSM265, an inhibitor of Plasmodium dihydroorotate dehydrogenase. To explore the mechanisms by which resistance might develop to DSM265 in the field, we selected for DSM265-resistant P. falciparum parasites in vitro. Any of five different amino acid changes led to reduced efficacy on the parasite and to decreased DSM265 binding to P. falciparum DHODH. The DSM265-resistant parasites retained full sensitivity to atovaquone. All but one of the observed mutations were in the DSM265 binding site, and the remaining C276F was in the adjacent flavin cofactor site. The C276F mutation was previously identified in a recrudescent parasite during a Phase IIa clinical study. We confirmed that this mutation (and the related C276Y) accounted for the full level of observed DSM265 resistance by regenerating the mutation using CRISPR/Cas9 genome editing. X-ray structure analysis of the C276F mutant enzyme showed that conformational changes of nearby residues were required to accommodate the larger F276 residue, which in turn led to a restriction in the size of the DSM265 binding pocket. These findings underscore the importance of developing DSM265 as part of a combination therapy with other agents for successful use against malaria.
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Affiliation(s)
- John White
- Departments of Chemistry and Global Health, University of Washington, 36 Bagley Hall, 400 15th Avenue NE, Seattle, Washington 98195, United States
| | - Satish K. Dhingra
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
| | - Xiaoyi Deng
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Farah El Mazouni
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Marcus C. S. Lee
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, U.K
| | - Gustavo A. Afanador
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Aloysus Lawong
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Diana R. Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Caroline L. Ng
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
| | - Jade Bath
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
| | - Pradipsinh K. Rathod
- Departments of Chemistry and Global Health, University of Washington, 36 Bagley Hall, 400 15th Avenue NE, Seattle, Washington 98195, United States
| | - David A. Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, PH8-W, 630 West 168th Street, PH 8-West, New York, New York 10032, United States
| | - Margaret A. Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
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28
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Fischer G. Recent advances in 1,2,4-triazolo[1,5-a]pyrimidine chemistry. ADVANCES IN HETEROCYCLIC CHEMISTRY 2019. [DOI: 10.1016/bs.aihch.2018.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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29
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Kokkonda S, El Mazouni F, White KL, White J, Shackleford DM, Lafuente-Monasterio MJ, Rowland P, Manjalanagara K, Joseph JT, Garcia-Pérez A, Fernandez J, Gamo FJ, Waterson D, Burrows JN, Palmer MJ, Charman SA, Rathod PK, Phillips MA. Isoxazolopyrimidine-Based Inhibitors of Plasmodium falciparum Dihydroorotate Dehydrogenase with Antimalarial Activity. ACS OMEGA 2018; 3:9227-9240. [PMID: 30197997 PMCID: PMC6120730 DOI: 10.1021/acsomega.8b01573] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 07/31/2018] [Indexed: 06/08/2023]
Abstract
Malaria kills nearly 0.5 million people yearly and impacts the lives of those living in over 90 countries where it is endemic. The current treatment programs are threatened by increasing drug resistance. Dihydroorotate dehydrogenase (DHODH) is now clinically validated as a target for antimalarial drug discovery as a triazolopyrimidine class inhibitor (DSM265) is currently undergoing clinical development. We discovered a related isoxazolopyrimidine series in a phenotypic screen, later determining that it targeted DHODH. To determine if the isoxazolopyrimidines could yield a drug candidate, we initiated hit-to-lead medicinal chemistry. Several potent analogues were identified, including a compound that showed in vivo antimalarial activity. The isoxazolopyrimidines were more rapidly metabolized than their triazolopyrimidine counterparts, and the pharmacokinetic data were not consistent with the goal of a single-dose treatment for malaria.
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Affiliation(s)
- Sreekanth Kokkonda
- Departments
of Chemistry and Global Health, University
of Washington, Seattle, Washington 98195, United States
| | - Farah El Mazouni
- Department
of Biochemistry, University of Texas Southwestern
Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9038, United States
| | - Karen L. White
- Centre
for Drug Candidate Optimisation, Monash
Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - John White
- Departments
of Chemistry and Global Health, University
of Washington, Seattle, Washington 98195, United States
| | - David M. Shackleford
- Centre
for Drug Candidate Optimisation, Monash
Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | | | - Paul Rowland
- Tres
Cantos Medicines Development Campus, GSK, Severo Ochoa, Madrid 28760, Spain
| | | | | | - Adolfo Garcia-Pérez
- Tres
Cantos Medicines Development Campus, GSK, Severo Ochoa, Madrid 28760, Spain
| | - Jorge Fernandez
- Tres
Cantos Medicines Development Campus, GSK, Severo Ochoa, Madrid 28760, Spain
| | | | - David Waterson
- Medicines
for Malaria Venture, 20, Route de Pré-Bois, 1215 Geneva, Switzerland
| | - Jeremy N. Burrows
- Medicines
for Malaria Venture, 20, Route de Pré-Bois, 1215 Geneva, Switzerland
| | - Michael J. Palmer
- Medicines
for Malaria Venture, 20, Route de Pré-Bois, 1215 Geneva, Switzerland
| | - Susan A. Charman
- Centre
for Drug Candidate Optimisation, Monash
Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Pradipsinh K. Rathod
- Departments
of Chemistry and Global Health, University
of Washington, Seattle, Washington 98195, United States
| | - Margaret A. Phillips
- Department
of Biochemistry, University of Texas Southwestern
Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9038, United States
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30
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Plasmodium falciparum dihydroorotate dehydrogenase: a drug target against malaria. Future Med Chem 2018; 10:1853-1874. [PMID: 30019917 DOI: 10.4155/fmc-2017-0250] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Malaria remains one of the most lethal infectious diseases worldwide, and the most severe form is caused by Plasmodium falciparum. In recent decades, the major challenge to treatment of this disease has been the ability of the protozoan parasite to develop resistance to the drugs that are currently in use. Among P. falciparum enzymes, P. falciparum dihydroorotate dehydrogenase has been identified as an important target in drug discovery. Interference with the activity of this enzyme inhibits de novo pyrimidine biosynthesis and consequently prevents malarial infection. Organic synthesis, x-ray crystallography, high-throughput screening and molecular modeling methods such as molecular docking, quantitative structure-activity relationships, structure-based pharmacophore mapping and molecular dynamics simulations have been applied to the discovery of new inhibitors of P. falciparum dihydroorotate dehydrogenase.
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31
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Lang L, Hu Q, Wang J, Liu Z, Huang J, Lu W, Huang Y. Coptisine, a natural alkaloid from Coptidis Rhizoma
, inhibits plasmodium falciparum dihydroorotate dehydrogenase. Chem Biol Drug Des 2018; 92:1324-1332. [DOI: 10.1111/cbdd.13197] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 01/22/2018] [Accepted: 03/17/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Li Lang
- Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; Shanghai China
| | - Qian Hu
- Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; Shanghai China
| | - Jingyuan Wang
- Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; Shanghai China
| | - Zehui Liu
- Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; Shanghai China
| | - Jin Huang
- Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; Shanghai China
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology; Institute of Biomedical Sciences and School of Life Sciences; East China Normal University; Shanghai China
| | - Ying Huang
- Guangdong Institute for Drug Control; Guangzhou Guangdong China
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32
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Meanwell NA. Fluorine and Fluorinated Motifs in the Design and Application of Bioisosteres for Drug Design. J Med Chem 2018; 61:5822-5880. [PMID: 29400967 DOI: 10.1021/acs.jmedchem.7b01788] [Citation(s) in RCA: 1339] [Impact Index Per Article: 223.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The electronic properties and relatively small size of fluorine endow it with considerable versatility as a bioisostere and it has found application as a substitute for lone pairs of electrons, the hydrogen atom, and the methyl group while also acting as a functional mimetic of the carbonyl, carbinol, and nitrile moieties. In this context, fluorine substitution can influence the potency, conformation, metabolism, membrane permeability, and P-gp recognition of a molecule and temper inhibition of the hERG channel by basic amines. However, as a consequence of the unique properties of fluorine, it features prominently in the design of higher order structural metaphors that are more esoteric in their conception and which reflect a more sophisticated molecular construction that broadens biological mimesis. In this Perspective, applications of fluorine in the construction of bioisosteric elements designed to enhance the in vitro and in vivo properties of a molecule are summarized.
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Affiliation(s)
- Nicholas A Meanwell
- Discovery Chemistry and Molecular Technologies Bristol-Myers Squibb Research and Development P.O. Box 4000, Princeton , New Jersey 08543-4000 , United States
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Brandão GC, Rocha Missias FC, Arantes LM, Soares LF, Roy KK, Doerksen RJ, Braga de Oliveira A, Pereira GR. Antimalarial naphthoquinones. Synthesis via click chemistry, in vitro activity , docking to Pf DHODH and SAR of lapachol-based compounds. Eur J Med Chem 2018; 145:191-205. [DOI: 10.1016/j.ejmech.2017.12.051] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 12/11/2017] [Accepted: 12/13/2017] [Indexed: 11/29/2022]
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+Targeting Mitochondrial Functions as Antimalarial Regime, What Is Next? CURRENT CLINICAL MICROBIOLOGY REPORTS 2017. [DOI: 10.1007/s40588-017-0075-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Interconvertible geometric isomers of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors exhibit multiple binding modes. Bioorg Med Chem Lett 2017; 27:3878-3882. [DOI: 10.1016/j.bmcl.2017.06.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/15/2017] [Accepted: 06/17/2017] [Indexed: 11/21/2022]
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36
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Manhas A, Lone MY, Jha PC. Multicomplex-based pharmacophore modeling coupled with molecular dynamics simulations: An efficient strategy for the identification of novel inhibitors of Pf DHODH. J Mol Graph Model 2017; 75:413-423. [DOI: 10.1016/j.jmgm.2017.04.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/17/2017] [Accepted: 04/18/2017] [Indexed: 01/08/2023]
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Carey MA, Papin JA, Guler JL. Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance. BMC Genomics 2017; 18:543. [PMID: 28724354 PMCID: PMC5518114 DOI: 10.1186/s12864-017-3905-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/27/2017] [Indexed: 02/06/2023] Open
Abstract
Background Malaria remains a major public health burden and resistance has emerged to every antimalarial on the market, including the frontline drug, artemisinin. Our limited understanding of Plasmodium biology hinders the elucidation of resistance mechanisms. In this regard, systems biology approaches can facilitate the integration of existing experimental knowledge and further understanding of these mechanisms. Results Here, we developed a novel genome-scale metabolic network reconstruction, iPfal17, of the asexual blood-stage P. falciparum parasite to expand our understanding of metabolic changes that support resistance. We identified 11 metabolic tasks to evaluate iPfal17 performance. Flux balance analysis and simulation of gene knockouts and enzyme inhibition predict candidate drug targets unique to resistant parasites. Moreover, integration of clinical parasite transcriptomes into the iPfal17 reconstruction reveals patterns associated with antimalarial resistance. These results predict that artemisinin sensitive and resistant parasites differentially utilize scavenging and biosynthetic pathways for multiple essential metabolites, including folate and polyamines. Our findings are consistent with experimental literature, while generating novel hypotheses about artemisinin resistance and parasite biology. We detect evidence that resistant parasites maintain greater metabolic flexibility, perhaps representing an incomplete transition to the metabolic state most appropriate for nutrient-rich blood. Conclusion Using this systems biology approach, we identify metabolic shifts that arise with or in support of the resistant phenotype. This perspective allows us to more productively analyze and interpret clinical expression data for the identification of candidate drug targets for the treatment of resistant parasites. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3905-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maureen A Carey
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, School of Medicine, Charlottesville, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, USA.
| | - Jennifer L Guler
- Department of Biology, University of Virginia, Charlottesville, USA. .,Division of Infectious Diseases and International Health, University of Virginia, School of Medicine, Charlottesville, USA.
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38
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Reis RAG, Calil FA, Feliciano PR, Pinheiro MP, Nonato MC. The dihydroorotate dehydrogenases: Past and present. Arch Biochem Biophys 2017; 632:175-191. [PMID: 28666740 DOI: 10.1016/j.abb.2017.06.019] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/23/2017] [Accepted: 06/26/2017] [Indexed: 01/24/2023]
Abstract
The flavoenzyme dihydroorotate dehydrogenase catalyzes the stereoselective oxidation of (S)-dihydroorotate to orotate in the fourth of the six conserved enzymatic reactions involved in the de novo pyrimidine biosynthetic pathway. Inhibition of pyrimidine metabolism by selectively targeting DHODHs has been exploited in the development of new therapies against cancer, immunological disorders, bacterial and viral infections, and parasitic diseases. Through a chronological narrative, this review summarizes the efforts of the scientific community to achieve our current understanding of structural and biochemical properties of DHODHs. It also attempts to describe the latest advances in medicinal chemistry for therapeutic development based on the selective inhibition of DHODH, including an overview of the experimental techniques used for ligand screening during the process of drug discovery.
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Affiliation(s)
- Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Felipe Antunes Calil
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, 14040-903, Brazil
| | - Patricia Rosa Feliciano
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Matheus Pinto Pinheiro
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, 13083-970, Brazil
| | - M Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, 14040-903, Brazil.
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Maetani M, Kato N, Jabor VAP, Calil FA, Nonato MC, Scherer CA, Schreiber SL. Discovery of Antimalarial Azetidine-2-carbonitriles That Inhibit P. falciparum Dihydroorotate Dehydrogenase. ACS Med Chem Lett 2017; 8:438-442. [PMID: 28435533 PMCID: PMC5392761 DOI: 10.1021/acsmedchemlett.7b00030] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/27/2017] [Indexed: 12/15/2022] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is an enzyme necessary for pyrimidine biosynthesis in protozoan parasites of the genus Plasmodium, the causative agents of malaria. We recently reported the identification of novel compounds derived from diversity-oriented synthesis with activity in multiple stages of the malaria parasite life cycle. Here, we report the optimization of a potent series of antimalarial inhibitors consisting of azetidine-2-carbonitriles, which we had previously shown to target P. falciparum DHODH in a biochemical assay. Optimized compound BRD9185 (27) has in vitro activity against multidrug-resistant blood-stage parasites (EC50 = 0.016 μM) and is curative after just three doses in a P. berghei mouse model. BRD9185 has a long half-life (15 h) and low clearance in mice and represents a new structural class of DHODH inhibitors with potential as antimalarial drugs.
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Affiliation(s)
- Micah Maetani
- Department of Chemistry
and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Broad Institute, Cambridge, Massachusetts 02142, United States
| | - Nobutaka Kato
- Broad Institute, Cambridge, Massachusetts 02142, United States
| | - Valquiria A. P. Jabor
- School of Pharmaceutical Sciences of Ribeirão
Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Felipe A. Calil
- School of Pharmaceutical Sciences of Ribeirão
Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Maria Cristina Nonato
- School of Pharmaceutical Sciences of Ribeirão
Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | | | - Stuart L. Schreiber
- Department of Chemistry
and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Broad Institute, Cambridge, Massachusetts 02142, United States
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02138, United States
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40
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Phillips MA, White KL, Kokkonda S, Deng X, White J, El Mazouni F, Marsh K, Tomchick DR, Manjalanagara K, Rudra KR, Wirjanata G, Noviyanti R, Price RN, Marfurt J, Shackleford DM, Chiu FCK, Campbell M, Jimenez-Diaz MB, Bazaga SF, Angulo-Barturen I, Martinez MS, Lafuente-Monasterio M, Kaminsky W, Silue K, Zeeman AM, Kocken C, Leroy D, Blasco B, Rossignol E, Rueckle T, Matthews D, Burrows JN, Waterson D, Palmer MJ, Rathod PK, Charman SA. A Triazolopyrimidine-Based Dihydroorotate Dehydrogenase Inhibitor with Improved Drug-like Properties for Treatment and Prevention of Malaria. ACS Infect Dis 2016; 2:945-957. [PMID: 27641613 DOI: 10.1021/acsinfecdis.6b00144] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The emergence of drug-resistant malaria parasites continues to hamper efforts to control this lethal disease. Dihydroorotate dehydrogenase has recently been validated as a new target for the treatment of malaria, and a selective inhibitor (DSM265) of the Plasmodium enzyme is currently in clinical development. With the goal of identifying a backup compound to DSM265, we explored replacement of the SF5-aniline moiety of DSM265 with a series of CF3-pyridinyls while maintaining the core triazolopyrimidine scaffold. This effort led to the identification of DSM421, which has improved solubility, lower intrinsic clearance, and increased plasma exposure after oral dosing compared to DSM265, while maintaining a long predicted human half-life. Its improved physical and chemical properties will allow it to be formulated more readily than DSM265. DSM421 showed excellent efficacy in the SCID mouse model of P. falciparum malaria that supports the prediction of a low human dose (<200 mg). Importantly DSM421 showed equal activity against both P. falciparum and P. vivax field isolates, while DSM265 was more active on P. falciparum. DSM421 has the potential to be developed as a single-dose cure or once-weekly chemopreventative for both P. falciparum and P. vivax malaria, leading to its advancement as a preclinical development candidate.
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Affiliation(s)
| | - Karen L. White
- Centre
for Drug Candidate Optimisation, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Sreekanth Kokkonda
- Departments
of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | | | - John White
- Departments
of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | | | - Kennan Marsh
- AbbVie Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064-6104, United States
| | | | | | | | - Grennady Wirjanata
- Global
and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, P.O. Box 41096, Casuarina, NT 0811, Australia
| | - Rintis Noviyanti
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, 10430 Jakarta, Indonesia
| | - Ric N. Price
- Global
and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, P.O. Box 41096, Casuarina, NT 0811, Australia
- Centre
for Tropical Medicine and Global Health, Nuffield Department of Clinical
Medicine, University of Oxford, Oxford OX3 7LJ, U.K
| | - Jutta Marfurt
- Global
and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, P.O. Box 41096, Casuarina, NT 0811, Australia
| | - David M. Shackleford
- Centre
for Drug Candidate Optimisation, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Francis C. K. Chiu
- Centre
for Drug Candidate Optimisation, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Michael Campbell
- Centre
for Drug Candidate Optimisation, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, VIC 3052, Australia
| | | | - Santiago Ferrer Bazaga
- GlaxoSmithKline, Tres Cantos Medicines Development
Campus, Severo Ochoa, Madrid 28760, Spain
| | - Iñigo Angulo-Barturen
- GlaxoSmithKline, Tres Cantos Medicines Development
Campus, Severo Ochoa, Madrid 28760, Spain
| | - Maria Santos Martinez
- GlaxoSmithKline, Tres Cantos Medicines Development
Campus, Severo Ochoa, Madrid 28760, Spain
| | | | - Werner Kaminsky
- Departments
of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Kigbafori Silue
- Centre Suisse de Recherches Scientifiques en Côte d’Ivoire, Km17, Route de Dabou, Adiopodoumé, BP 1303 Abidjan, Ivory Coast
| | - Anne-Marie Zeeman
- Biomedical Primate Research Centre, 2288 GJ Rijswijk, The Netherlands
| | - Clemens Kocken
- Biomedical Primate Research Centre, 2288 GJ Rijswijk, The Netherlands
| | - Didier Leroy
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | | | | | - Dave Matthews
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | | | | | - Pradipsinh K. Rathod
- Departments
of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Susan A. Charman
- Centre
for Drug Candidate Optimisation, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, VIC 3052, Australia
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Dickerman BK, Elsworth B, Cobbold SA, Nie CQ, McConville MJ, Crabb BS, Gilson PR. Identification of inhibitors that dually target the new permeability pathway and dihydroorotate dehydrogenase in the blood stage of Plasmodium falciparum. Sci Rep 2016; 6:37502. [PMID: 27874068 PMCID: PMC5118696 DOI: 10.1038/srep37502] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/28/2016] [Indexed: 12/22/2022] Open
Abstract
Plasmodium parasites are responsible for the devastating disease malaria that affects hundreds of millions of people each year. Blood stage parasites establish new permeability pathways (NPPs) in infected red blood cell membranes to facilitate the uptake of nutrients and removal of parasite waste products. Pharmacological inhibition of the NPPs is expected to lead to nutrient starvation and accumulation of toxic metabolites resulting in parasite death. Here, we have screened a curated library of antimalarial compounds, the MMV Malaria Box, identifying two compounds that inhibit NPP function. Unexpectedly, metabolic profiling suggested that both compounds also inhibit dihydroorotate dehydrogense (DHODH), which is required for pyrimidine synthesis and is a validated drug target in its own right. Expression of yeast DHODH, which bypasses the need for the parasite DHODH, increased parasite resistance to these compounds. These studies identify two potential candidates for therapeutic development that simultaneously target two essential pathways in Plasmodium, NPP and DHODH.
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Affiliation(s)
| | - Brendan Elsworth
- Burnet Institute, Melbourne, Victoria, Australia
- Monash University, Clayton, Victoria, Australia
| | - Simon A. Cobbold
- Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia
| | | | - Malcolm J. McConville
- Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia
| | - Brendan S. Crabb
- Burnet Institute, Melbourne, Victoria, Australia
- Monash University, Clayton, Victoria, Australia
- Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia
| | - Paul R. Gilson
- Burnet Institute, Melbourne, Victoria, Australia
- Monash University, Clayton, Victoria, Australia
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42
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Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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Evaluation of 7-arylaminopyrazolo[1,5-a]pyrimidines as anti-Plasmodium falciparum, antimalarial, and Pf-dihydroorotate dehydrogenase inhibitors. Eur J Med Chem 2016; 126:72-83. [PMID: 27744189 DOI: 10.1016/j.ejmech.2016.09.073] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 11/24/2022]
Abstract
Malaria remains one of the most serious global infectious diseases. An important target for antimalarial chemotherapy is the enzyme dihydroorotate dehydrogenase from Plasmodium falciparum (PfDHODH), which is responsible for the conversion of dihydroorotate to orotate in the de novo pyrimidine biosynthetic pathway. In this study, we have designed and synthesized fifteen 7-arylpyrazolo[1,5-a]pyrimidine derivatives using ring bioisosteric replacement and molecular hybridization of functional groups based on the highly active 5-methyl-N-(naphthalen-2-yl)-2-(trifluoromethyl)- [1,2,4]triazolo[1,5-a]pyrimidin-7-amine. The compounds were tested against Plasmodium falciparum, as antimalarials in mice with P. berghei, and as inhibitors of PfDHODH. Thirteen compounds were found to be active against P. falciparum, with IC50 values ranging from 1.2 ± 0.3 to 92 ± 26 μM in the anti-HRP2 and hypoxanthine assays. Four compounds showed the highest selective index (SI), which is a ratio between cytotoxicity and activity in vitro. The inhibition of PfDHODH showed that compound 30 (R2 = CH3; R5 = CF3; Ar = 7-β-naphthyl) displayed higher and selective inhibitory activity, with IC50 = 0.16 ± 0.01 μM, followed by 25 (R2 = CH3; R5 = CH3; Ar = 7-β-Naphthyl) and 19 (R2 = CF3; R5 = CF3; Ar = 7-β-naphthyl), with IC50 = 4 ± 1 μM and 6 ± 1 μM, respectively. The trifluoromethyl group at the 2- or 5-positions of the pyrazolo[1,5-a]pyrimidine ring led to increased drug activity. The docking results agreed with the values obtained from enzymatic assays.
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44
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Pyrimidine Pathway-Dependent and -Independent Functions of the Toxoplasma gondii Mitochondrial Dihydroorotate Dehydrogenase. Infect Immun 2016; 84:2974-81. [PMID: 27481247 DOI: 10.1128/iai.00187-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/25/2016] [Indexed: 11/20/2022] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) mediates the fourth step of de novo pyrimidine biosynthesis and is a proven drug target for inducing immunosuppression in therapy of human disease as well as a rapidly emerging drug target for treatment of malaria. In Toxoplasma gondii, disruption of the first, fifth, or sixth step of de novo pyrimidine biosynthesis induced uracil auxotrophy. However, previous attempts to generate uracil auxotrophy by genetically deleting the mitochondrion-associated DHODH of T. gondii (TgDHODH) failed. To further address the essentiality of TgDHODH, mutant gene alleles deficient in TgDHODH activity were designed to ablate the enzyme activity. Replacement of the endogenous DHODH gene with catalytically deficient DHODH gene alleles induced uracil auxotrophy. Catalytically deficient TgDHODH localized to the mitochondria, and parasites retained mitochondrial membrane potential. These results show that TgDHODH is essential for the synthesis of pyrimidines and suggest that TgDHODH is required for a second essential function independent of its role in pyrimidine biosynthesis.
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45
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Vyas VK, Qureshi G, Ghate M, Patel H, Dalai S. Identification of novel PfDHODH inhibitors as antimalarial agents via pharmacophore-based virtual screening followed by molecular docking and in vivo antimalarial activity. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2016; 27:427-440. [PMID: 27310104 DOI: 10.1080/1062936x.2016.1189959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/11/2016] [Indexed: 06/06/2023]
Abstract
Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) catalyses the fourth reaction of de novo pyrimidine biosynthesis in parasites, and represents an important target for the treatment of malaria. In this study, we describe pharmacophore-based virtual screening combined with docking study and biological evaluation as a rational strategy for identification of novel hits as antimalarial agents. Pharmacophore models were established from known PfDHODH inhibitors using the GALAHAD module with IC50 values ranging from 0.033 μM to 142 μM. The best pharmacophore model consisted of three hydrogen bond acceptor, one hydrogen bond donor and one hydrophobic features. The pharmacophore models were validated through receiver operating characteristic and Günere-Henry scoring methods. The best pharmacophore model as a 3D search query was searched against the IBS database. Several compounds with different structures (scaffolds) were retrieved as hit molecules. Among these compounds, those with a QFIT value of more than 81 were docked in the PfDHODH enzyme to further explore the binding modes of these compounds. In silico pharmacokinetic and toxicities were predicted for the best docked molecules. Finally, the identified hits were evaluated in vivo for their antimalarial activity in a parasite inhibition assay. The hits reported here showed good potential to become novel antimalarial agents.
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Affiliation(s)
- V K Vyas
- a Department of Pharmaceutical Chemistry , Institute of Pharmacy, Nirma University , Ahmedabad , India
| | - G Qureshi
- a Department of Pharmaceutical Chemistry , Institute of Pharmacy, Nirma University , Ahmedabad , India
| | - M Ghate
- a Department of Pharmaceutical Chemistry , Institute of Pharmacy, Nirma University , Ahmedabad , India
| | - H Patel
- b Institute of Science, Nirma University , Ahmedabad , India
| | - S Dalai
- b Institute of Science, Nirma University , Ahmedabad , India
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Kokkonda S, Deng X, White KL, Coteron JM, Marco M, de Las Heras L, White J, El Mazouni F, Tomchick DR, Manjalanagara K, Rudra KR, Chen G, Morizzi J, Ryan E, Kaminsky W, Leroy D, Martínez-Martínez MS, Jimenez-Diaz MB, Bazaga SF, Angulo-Barturen I, Waterson D, Burrows JN, Matthews D, Charman SA, Phillips MA, Rathod PK. Tetrahydro-2-naphthyl and 2-Indanyl Triazolopyrimidines Targeting Plasmodium falciparum Dihydroorotate Dehydrogenase Display Potent and Selective Antimalarial Activity. J Med Chem 2016; 59:5416-31. [PMID: 27127993 PMCID: PMC4904246 DOI: 10.1021/acs.jmedchem.6b00275] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Malaria persists as one of the most devastating global infectious diseases. The pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) has been identified as a new malaria drug target, and a triazolopyrimidine-based DHODH inhibitor 1 (DSM265) is in clinical development. We sought to identify compounds with higher potency against Plasmodium DHODH while showing greater selectivity toward animal DHODHs. Herein we describe a series of novel triazolopyrimidines wherein the p-SF5-aniline was replaced with substituted 1,2,3,4-tetrahydro-2-naphthyl or 2-indanyl amines. These compounds showed strong species selectivity, and several highly potent tetrahydro-2-naphthyl derivatives were identified. Compounds with halogen substitutions displayed sustained plasma levels after oral dosing in rodents leading to efficacy in the P. falciparum SCID mouse malaria model. These data suggest that tetrahydro-2-naphthyl derivatives have the potential to be efficacious for the treatment of malaria, but due to higher metabolic clearance than 1, they most likely would need to be part of a multidose regimen.
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Affiliation(s)
- Sreekanth Kokkonda
- Departments of Chemistry and Global Health, University of Washington , Seattle, Washington 98195, United States
| | | | - Karen L White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Jose M Coteron
- GSK , Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760 Spain
| | - Maria Marco
- GSK , Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760 Spain
| | - Laura de Las Heras
- GSK , Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760 Spain
| | - John White
- Departments of Chemistry and Global Health, University of Washington , Seattle, Washington 98195, United States
| | | | | | | | | | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Julia Morizzi
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Eileen Ryan
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Werner Kaminsky
- Departments of Chemistry and Global Health, University of Washington , Seattle, Washington 98195, United States
| | - Didier Leroy
- Medicines for Malaria Venture , 1215 Geneva, Switzerland
| | | | | | | | | | - David Waterson
- Medicines for Malaria Venture , 1215 Geneva, Switzerland
| | | | - Dave Matthews
- 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
| | | | - Pradipsinh K Rathod
- Departments of Chemistry and Global Health, University of Washington , Seattle, Washington 98195, United States
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Phillips MA, Lotharius J, Marsh K, White J, Dayan A, White KL, Njoroge JW, El Mazouni F, Lao Y, Kokkonda S, Tomchick DR, Deng X, Laird T, Bhatia SN, March S, Ng CL, Fidock DA, Wittlin S, Lafuente-Monasterio M, Benito FJG, Alonso LMS, Martinez MS, Jimenez-Diaz MB, Bazaga SF, Angulo-Barturen I, Haselden JN, Louttit J, Cui Y, Sridhar A, Zeeman AM, Kocken C, Sauerwein R, Dechering K, Avery VM, Duffy S, Delves M, Sinden R, Ruecker A, Wickham KS, Rochford R, Gahagen J, Iyer L, Riccio E, Mirsalis J, Bathhurst I, Rueckle T, Ding X, Campo B, Leroy D, Rogers MJ, Rathod PK, Burrows JN, Charman SA. A long-duration dihydroorotate dehydrogenase inhibitor (DSM265) for prevention and treatment of malaria. Sci Transl Med 2016; 7:296ra111. [PMID: 26180101 DOI: 10.1126/scitranslmed.aaa6645] [Citation(s) in RCA: 217] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Malaria is one of the most significant causes of childhood mortality, but disease control efforts are threatened by resistance of the Plasmodium parasite to current therapies. Continued progress in combating malaria requires development of new, easy to administer drug combinations with broad-ranging activity against all manifestations of the disease. DSM265, a triazolopyrimidine-based inhibitor of the pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH), is the first DHODH inhibitor to reach clinical development for treatment of malaria. We describe studies profiling the biological activity, pharmacological and pharmacokinetic properties, and safety of DSM265, which supported its advancement to human trials. DSM265 is highly selective toward DHODH of the malaria parasite Plasmodium, efficacious against both blood and liver stages of P. falciparum, and active against drug-resistant parasite isolates. Favorable pharmacokinetic properties of DSM265 are predicted to provide therapeutic concentrations for more than 8 days after a single oral dose in the range of 200 to 400 mg. DSM265 was well tolerated in repeat-dose and cardiovascular safety studies in mice and dogs, was not mutagenic, and was inactive against panels of human enzymes/receptors. The excellent safety profile, blood- and liver-stage activity, and predicted long half-life in humans position DSM265 as a new potential drug combination partner for either single-dose treatment or once-weekly chemoprevention. DSM265 has advantages over current treatment options that are dosed daily or are inactive against the parasite liver stage.
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Affiliation(s)
- Margaret A Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, TX 75390-9041, USA.
| | | | - Kennan Marsh
- Abbvie, 1 North Waukegan Road, North Chicago, IL 60064-6104, USA
| | - John White
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA 98195, USA
| | - Anthony Dayan
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Karen L White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Jacqueline W Njoroge
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, TX 75390-9041, USA
| | - Farah El Mazouni
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, TX 75390-9041, USA
| | - Yanbin Lao
- Abbvie, 1 North Waukegan Road, North Chicago, IL 60064-6104, USA
| | - Sreekanth Kokkonda
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA 98195, USA
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA
| | - Xiaoyi Deng
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, TX 75390-9041, USA
| | - Trevor Laird
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Sangeeta N Bhatia
- Health Sciences and Technology/Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sandra March
- Health Sciences and Technology/Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Caroline L Ng
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA. Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland. University of Basel, 4003 Basel, Switzerland
| | | | | | - Laura Maria Sanz Alonso
- GlaxoSmithKline (GSK), Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | - Maria Santos Martinez
- GlaxoSmithKline (GSK), Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | - Maria Belen Jimenez-Diaz
- GlaxoSmithKline (GSK), Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | - Santiago Ferrer Bazaga
- GlaxoSmithKline (GSK), Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | - Iñigo Angulo-Barturen
- GlaxoSmithKline (GSK), Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | - John N Haselden
- GlaxoSmithKline (GSK), Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | | | - Yi Cui
- GSK, Park Road, Ware, Hertfordshire SG12 0DP, UK
| | - Arun Sridhar
- GSK, Park Road, Ware, Hertfordshire SG12 0DP, UK
| | - Anna-Marie Zeeman
- Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH Rijswijk, Netherlands
| | - Clemens Kocken
- Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH Rijswijk, Netherlands
| | | | | | - Vicky M Avery
- Discovery Biology, Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Sandra Duffy
- Discovery Biology, Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Michael Delves
- Imperial College of Science Technology and Medicine, London SW7 2AY, UK
| | - Robert Sinden
- Imperial College of Science Technology and Medicine, London SW7 2AY, UK
| | - Andrea Ruecker
- Imperial College of Science Technology and Medicine, London SW7 2AY, UK
| | - Kristina S Wickham
- State University of New York Upstate Medical University, Syracuse, NY 13210, USA
| | - Rosemary Rochford
- State University of New York Upstate Medical University, Syracuse, NY 13210, USA
| | | | | | - Ed Riccio
- SRI International, Menlo Park, CA 94025, USA
| | | | - Ian Bathhurst
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | - Xavier Ding
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Brice Campo
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Didier Leroy
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - M John Rogers
- National Institutes for Allergy and Infectious Diseases, 6610 Rockledge Drive, Bethesda, MD 20892, USA
| | - Pradipsinh K Rathod
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA 98195, USA
| | | | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia.
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Pavadai E, El Mazouni F, Wittlin S, de Kock C, Phillips MA, Chibale K. Identification of New Human Malaria Parasite Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors by Pharmacophore and Structure-Based Virtual Screening. J Chem Inf Model 2016; 56:548-62. [PMID: 26915022 DOI: 10.1021/acs.jcim.5b00680] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH), a key enzyme in the de novo pyrimidine biosynthesis pathway, which the Plasmodium falciparum relies on exclusively for survival, has emerged as a promising target for antimalarial drugs. In an effort to discover new and potent PfDHODH inhibitors, 3D-QSAR pharmacophore models were developed based on the structures of known PfDHODH inhibitors and the validated Hypo1 model was used as a 3D search query for virtual screening of the National Cancer Institute database. The virtual hit compounds were further filtered based on molecular docking and Molecular Mechanics/Generalized Born Surface Area binding energy calculations. The combination of the pharmacophore and structure-based virtual screening resulted in the identification of nine new compounds that showed >25% inhibition of PfDHODH at a concentration of 10 μM, three of which exhibited IC50 values in the range of 0.38-20 μM. The most active compound, NSC336047, displayed species-selectivity for PfDHODH over human DHODH and inhibited parasite growth with an IC50 of 26 μM. In addition to this, 13 compounds inhibited parasite growth with IC50 values of ≤ 50 μM, 4 of which showed IC50 values in the range of 5-12 μM. These compounds could be further explored in the identification and development of more potent PfDHODH and parasite growth inhibitors.
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Affiliation(s)
| | - Farah El Mazouni
- Departments of Pharmacology, University of Texas Southwestern Medical Center at Dallas , 6001 Forest Park Blvd, Dallas, Texas 75390-9041, United States
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute , Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel , 4002 Basel, Switzerland
| | - Carmen de Kock
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town , Observatory 7925, South Africa
| | - Margaret A Phillips
- Departments of Pharmacology, University of Texas Southwestern Medical Center at Dallas , 6001 Forest Park Blvd, Dallas, Texas 75390-9041, United States
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Hou X, Chen X, Zhang M, Yan A. QSAR study on the antimalarial activity of Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2016; 27:101-124. [PMID: 26911561 DOI: 10.1080/1062936x.2015.1134652] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Plasmodium falciparum, the most fatal parasite that causes malaria, is responsible for over one million deaths per year. P. falciparum dihydroorotate dehydrogenase (PfDHODH) has been validated as a promising drug development target for antimalarial therapy since it catalyzes the rate-limiting step for DNA and RNA biosynthesis. In this study, we investigated the quantitative structure-activity relationships (QSAR) of the antimalarial activity of PfDHODH inhibitors by generating four computational models using a multilinear regression (MLR) and a support vector machine (SVM) based on a dataset of 255 PfDHODH inhibitors. All the models display good prediction quality with a leave-one-out q(2) >0.66, a correlation coefficient (r) >0.85 on both training sets and test sets, and a mean square error (MSE) <0.32 on training sets and <0.37 on test sets, respectively. The study indicated that the hydrogen bonding ability, atom polarizabilities and ring complexity are predominant factors for inhibitors' antimalarial activity. The models are capable of predicting inhibitors' antimalarial activity and the molecular descriptors for building the models could be helpful in the development of new antimalarial drugs.
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Affiliation(s)
- X Hou
- a State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering , Beijing University of Chemical Technology , Beijing , P.R. China
| | - X Chen
- a State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering , Beijing University of Chemical Technology , Beijing , P.R. China
| | - M Zhang
- a State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering , Beijing University of Chemical Technology , Beijing , P.R. China
| | - A Yan
- a State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering , Beijing University of Chemical Technology , Beijing , P.R. China
- b Stake Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing , P.R. China
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Koes DR, Pabon NA, Deng X, Phillips MA, Camacho CJ. A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool. PLoS One 2015; 10:e0134697. [PMID: 26258606 PMCID: PMC4530941 DOI: 10.1371/journal.pone.0134697] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/13/2015] [Indexed: 01/09/2023] Open
Abstract
The 2012 Teach-Discover-Treat (TDT) community-wide experiment provided a unique opportunity to test prospective virtual screening protocols targeting the anti-malarial target dihydroorotate dehydrogenase (DHODH). Facilitated by ZincPharmer, an open access online interactive pharmacophore search of the ZINC database, the experience resulted in the development of a novel classification scheme that successfully predicted the bound structure of a non-triazolopyrimidine inhibitor, as well as an overall hit rate of 27% of tested active compounds from multiple novel chemical scaffolds. The general approach entailed exhaustively building and screening sparse pharmacophore models comprising of a minimum of three features for each bound ligand in all available DHODH co-crystals and iteratively adding features that increased the number of known binders returned by the query. Collectively, the TDT experiment provided a unique opportunity to teach computational methods of drug discovery, develop innovative methodologies and prospectively discover new compounds active against DHODH.
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Affiliation(s)
- David Ryan Koes
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States of America
- * E-mail: (DRK); (CJC)
| | - Nicolas A. Pabon
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Xiaoyi Deng
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Blvd, Dallas, TX, United States of America
| | - Margaret A. Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Blvd, Dallas, TX, United States of America
| | - Carlos J. Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States of America
- * E-mail: (DRK); (CJC)
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