1
|
Talbott JM, Tessier BR, Harding EE, Walby GD, Hess KJ, Baskevics V, Katkevics M, Rozners E, MacKay JA. Improved Triplex-Forming Isoorotamide PNA Nucleobases for A-U Recognition of RNA Duplexes. Chemistry 2023; 29:e202302390. [PMID: 37647091 DOI: 10.1002/chem.202302390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Four new isoorotamide (Io)-containing PNA nucleobases have been designed for A-U recognition of double helical RNA. New PNA monomers were prepared efficiently and incorporated into PNA nonamers for binding A-U in a PNA:RNA2 triplex. Isothermal titration calorimetry and UV thermal melting experiments revealed slightly improved binding affinity for singly modified PNA compared to known A-binding nucleobases. Molecular dynamics simulations provided further insights into binding of Io bases in the triple helix. Together, the data revealed interesting insights into binding modes including the notion that three Hoogsteen hydrogen bonds are unnecessary for strong selective binding of an extended nucleobase. Cationic monomer Io8 additionally gave the highest affinity observed for an A-binding nucleobase to date. These results will help inform future nucleobase design toward the goal of recognizing any sequence of double helical RNA.
Collapse
Affiliation(s)
- John M Talbott
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | - Brandon R Tessier
- Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA
| | - Emily E Harding
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | - Grant D Walby
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | - Kyle J Hess
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| | | | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA
| | - James A MacKay
- Department of Chemistry and Biochemistry, Elizabethtown College, Elizabethtown, PA 17022, USA
| |
Collapse
|
2
|
Rathod GK, Jain M, Sharma KK, Das S, Basak A, Jain R. New structural classes of antimalarials. Eur J Med Chem 2022; 242:114653. [PMID: 35985254 DOI: 10.1016/j.ejmech.2022.114653] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/22/2022] [Accepted: 07/31/2022] [Indexed: 11/19/2022]
Abstract
Malaria remains a major vector borne disease claiming millions of lives worldwide due to infections caused by Plasmodium sp. Discovery and development of antimalarial drugs have previously been dominated majorly by single drug therapy. The malaria parasite has developed resistance against first line and second line antimalarial drugs used in the single drug therapy. This has drawn attention to find ways to alleviate the disease burden supplanted by combination therapy with multiple drugs to overcome drug resistance. Emergence of resistant strains even against the combination therapy has now mandated the revision of the current antimalarial pharmacotherapy. Research efforts of the past decade led to the discovery and identification of several new structural classes of antimalarial agents with improved biological attributes over the older ones. The following is a comprehensive review, addressed to the new structural classes of heterocyclic and natural compounds that have been identified during the last decade as antimalarial agents. Some of the classes included herein contain one or more pharmacophores amalgamated into a single bioactive scaffold as antimalarial agents, which act upon the conventional and novel targets.
Collapse
Affiliation(s)
- Gajanan K Rathod
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab, 160 062, India
| | - Meenakshi Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab, 160 062, India
| | - Krishna K Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab, 160 062, India
| | - Samarpita Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab, 160 062, India
| | - Ahana Basak
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab, 160 062, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab, 160 062, India.
| |
Collapse
|
3
|
Fluorescent cyanine-guanidiniocarbonyl-pyrrole conjugate with pH-dependent DNA/RNA recognition and DPP III fluorescent labelling and inhibition properties. MONATSHEFTE FUR CHEMIE 2018. [DOI: 10.1007/s00706-018-2192-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
4
|
Matić J, Šupljika F, Tir N, Piotrowski P, Schmuck C, Abramić M, Piantanida I, Tomić S. Guanidiniocarbonyl-pyrrole-aryl conjugates as inhibitors of human dipeptidyl peptidase III: combined experimental and computational study. RSC Adv 2016. [DOI: 10.1039/c6ra16966j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Good overlap of the standard DPP III substrate Arg-Arg-2NA (magenta) and the most efficient novel inhibitor (guanidiniocarbonyl-pyrrole-pyrene conjugate, blue-red) in the DPP III binding site.
Collapse
Affiliation(s)
- Josipa Matić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Filip Šupljika
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Nora Tir
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Patryciusz Piotrowski
- Institute for Organic Chemistry
- University of Duisburg-Essen
- Universitässtrasse 7
- 45141 Essen
- Germany
| | - Carsten Schmuck
- Institute for Organic Chemistry
- University of Duisburg-Essen
- Universitässtrasse 7
- 45141 Essen
- Germany
| | - Marija Abramić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| |
Collapse
|
5
|
Aneja B, Kumar B, Jairajpuri MA, Abid M. A structure guided drug-discovery approach towards identification of Plasmodium inhibitors. RSC Adv 2016. [DOI: 10.1039/c5ra19673f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
This article provides a comprehensive review of inhibitors from natural, semisynthetic or synthetic sources against key targets ofPlasmodium falciparum.
Collapse
Affiliation(s)
- Babita Aneja
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Bhumika Kumar
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Mohammad Abid
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| |
Collapse
|
6
|
Ettari R, Pinto A, Tamborini L, Angelo IC, Grasso S, Zappalà M, Capodicasa N, Yzeiraj L, Gruber E, Aminake MN, Pradel G, Schirmeister T, De Micheli C, Conti P. Synthesis and biological evaluation of papain-family cathepsin L-like cysteine protease inhibitors containing a 1,4-benzodiazepine scaffold as antiprotozoal agents. ChemMedChem 2014; 9:1817-25. [PMID: 24919925 DOI: 10.1002/cmdc.201402079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Indexed: 11/10/2022]
Abstract
Novel papain-family cathepsin L-like cysteine protease inhibitors endowed with antitrypanosomal and antimalarial activity were developed, through an optimization study of previously developed inhibitors. In the present work, we studied the structure-activity relationships of these derivatives, with the aim to develop new analogues with a simplified and more synthetically accessible structure and with improved antiparasitic activity. The structure of the model compounds was significantly simplified by modifying or even eliminating the side chain appended at the C3 atom of the benzodiazepine scaffold. In addition, a simple methylene spacer of appropriate length was inserted between the benzodiazepine ring and the 3-bromoisoxazoline moiety. Several rhodesain and falcipain-2 inhibitors displaying single-digit micromolar or sub-micromolar antiparasitic activity against one or both parasites were identified, with activities that were one order of magnitude more potent than the model compounds.
Collapse
Affiliation(s)
- Roberta Ettari
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli, 25, 20133 Milano (Italy).
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Drug discovery and human African trypanosomiasis: a disease less neglected? Future Med Chem 2014; 5:1801-41. [PMID: 24144414 DOI: 10.4155/fmc.13.162] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Human African trypanosomiasis (HAT) has been neglected for a long time. The most recent drug to treat this disease, eflornithine, was approved by the US FDA in 2000. Current treatments exhibit numerous problematic side effects and are often ineffective against the debilitating CNS resident stage of the disease. Fortunately, several partnerships and initiatives have been formed over the last 20 years in an effort to eradicate HAT, along with a number of other neglected diseases. This has led to an increasing number of foundations and research institutions that are currently working on the development of new drugs for HAT and tools with which to diagnose and treat patients. New biochemical pathways as therapeutic targets are emerging, accompanied by increasing numbers of new antitrypanosomal compound classes. The future looks promising that this collaborative approach will facilitate eagerly awaited breakthroughs in the treatment of HAT.
Collapse
|
8
|
Lang S, Khalaf AI, Breen D, Huggan JK, Clements CJ, MacKay SP, Suckling CJ. Oligoamides of 2-amino-5-alkylthiazole 4-carboxylic acids: anti-trypanosomal compounds. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0723-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
9
|
Ettari R, Tamborini L, Angelo IC, Micale N, Pinto A, De Micheli C, Conti P. Inhibition of Rhodesain as a Novel Therapeutic Modality for Human African Trypanosomiasis. J Med Chem 2013; 56:5637-58. [DOI: 10.1021/jm301424d] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Roberta Ettari
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli
25, 20133 Milano, Italy
| | - Lucia Tamborini
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli
25, 20133 Milano, Italy
| | - Ilenia C. Angelo
- Dipartimento di Scienze del
Farmaco e Prodotti per la Salute, Università degli Studi di Messina, Viale Annunziata, 98168 Messina, Italy
| | - Nicola Micale
- Dipartimento di Scienze del
Farmaco e Prodotti per la Salute, Università degli Studi di Messina, Viale Annunziata, 98168 Messina, Italy
| | - Andrea Pinto
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli
25, 20133 Milano, Italy
| | - Carlo De Micheli
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli
25, 20133 Milano, Italy
| | - Paola Conti
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli
25, 20133 Milano, Italy
| |
Collapse
|