1
|
Sharma A, De Rosa M, Singla N, Singh G, Barnwal RP, Pandey A. Tuberculosis: An Overview of the Immunogenic Response, Disease Progression, and Medicinal Chemistry Efforts in the Last Decade toward the Development of Potential Drugs for Extensively Drug-Resistant Tuberculosis Strains. J Med Chem 2021; 64:4359-4395. [PMID: 33826327 DOI: 10.1021/acs.jmedchem.0c01833] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Tuberculosis (TB) is a slow growing, potentially debilitating disease that has plagued humanity for centuries and has claimed numerous lives across the globe. Concerted efforts by researchers have culminated in the development of various strategies to combat this malady. This review aims to raise awareness of the rapidly increasing incidences of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis, highlighting the significant modifications that were introduced in the TB treatment regimen over the past decade. A description of the role of pathogen-host immune mechanisms together with strategies for prevention of the disease is discussed. The struggle to develop novel drug therapies has continued in an effort to reduce the treatment duration, improve patient compliance and outcomes, and circumvent TB resistance mechanisms. Herein, we give an overview of the extensive medicinal chemistry efforts made during the past decade toward the discovery of new chemotypes, which are potentially active against TB-resistant strains.
Collapse
Affiliation(s)
- Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India.,UIPS, Panjab University, Chandigarh 160014, India
| | - Maria De Rosa
- Drug Discovery Unit, Ri.MED Foundation, Palermo 90133, Italy
| | - Neha Singla
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- UIPS, Panjab University, Chandigarh 160014, India
| | - Ravi P Barnwal
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| |
Collapse
|
2
|
Luo J, Chen P, Song C. An Overview of the Synthesis of Pyrazolotriazolopyrimidine Compounds. MINI-REV ORG CHEM 2020. [DOI: 10.2174/1570193x16666190723124839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pyrazolotriazolopyrimidines are an important class of nitrogen-containing heterocycles
that can act as a charismatic target and exhibit diverse pharmacological activities. These compounds
have received much attention because they are an attractive scaffold for the preparation of adenosine
receptor antagonists. Herein, we focus on an overview of the synthesis of these compounds with the
aim of assisting in the discovery of new pyrazolotriazolopyrimidine derivatives.
Collapse
Affiliation(s)
- Jin Luo
- Analytical and Testing Center, Jiangxi Normal University, Nanchang, Jiangxi 330022, China
| | - Puqing Chen
- Analytical and Testing Center, Jiangxi Normal University, Nanchang, Jiangxi 330022, China
| | - Chonghu Song
- Analytical and Testing Center, Jiangxi Normal University, Nanchang, Jiangxi 330022, China
| |
Collapse
|
3
|
Federico S, Margiotta E, Paoletta S, Kachler S, Klotz KN, Jacobson KA, Pastorin G, Moro S, Spalluto G. Pyrazolo[4,3- e][1,2,4]triazolo[1,5- c]pyrimidines to develop functionalized ligands to target adenosine receptors: fluorescent ligands as an example. MEDCHEMCOMM 2019; 10:1094-1108. [PMID: 31391881 PMCID: PMC6644567 DOI: 10.1039/c9md00014c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/16/2019] [Indexed: 01/07/2023]
Abstract
A series of adenosine receptor antagonists bearing a reactive linker was developed. Functionalization of these derivatives is useful to easily obtain multi-target ligands, receptor probes, drug delivery systems, and diagnostic or theranostic systems. The pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidine scaffold was chosen as a pharmacophore for the adenosine receptors. It was substituted at the 5 position with reactive linkers of different lengths. Then, these compounds were used to synthesise probes for the adenosine receptors by functionalization with a fluorescent moiety. Both series of compounds were evaluated for their binding at the four adenosine receptor subtypes. Different affinity and selectivity profiles were observed towards hA1, hA2A and hA3 adenosine receptors. In particular, fluorescent compounds behave as dual hA2A/hA3 ligands. Computational studies suggested different binding modes for developed compounds at the three receptors. Both molecular docking and supervised molecular dynamics (SuMD) simulations confirmed that the preferred binding mode at the single receptor was driven by the substitution present at the 5 position. Obtained results rationalized the compounds' binding profile at the adenosine receptors and pave the way for the development of more potent conjugable and conjugated ligands targeting these membrane receptors.
Collapse
Affiliation(s)
- Stephanie Federico
- Department of Chemical and Pharmaceutical Sciences , University of Trieste , Via Licio Giorgeri 1 , 34127 Trieste , Italy .
| | - Enrico Margiotta
- Molecular Modeling Section (MMS) , Dipartimento di Scienze del Farmaco , Università degli Studi di Padova , Via F. Marzolo 5 , 35131 Padova , Italy
| | - Silvia Paoletta
- Molecular Modeling Section (MMS) , Dipartimento di Scienze del Farmaco , Università degli Studi di Padova , Via F. Marzolo 5 , 35131 Padova , Italy
| | - Sonja Kachler
- Institut für Pharmakologie und Toxicologie , Universität Würzburg , Versbacher Straße 9 , 97078 Würzburg , Germany
| | - Karl-Norbert Klotz
- Institut für Pharmakologie und Toxicologie , Universität Würzburg , Versbacher Straße 9 , 97078 Würzburg , Germany
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry , National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892-0810 , USA
| | - Giorgia Pastorin
- Department of Pharmacy , National University of Singapore , 3 Science Drive 3 , 117543 Singapore
| | - Stefano Moro
- Molecular Modeling Section (MMS) , Dipartimento di Scienze del Farmaco , Università degli Studi di Padova , Via F. Marzolo 5 , 35131 Padova , Italy
| | - Giampiero Spalluto
- Department of Chemical and Pharmaceutical Sciences , University of Trieste , Via Licio Giorgeri 1 , 34127 Trieste , Italy .
| |
Collapse
|
4
|
Modi P, Patel S, Chhabria M. Structure-based design, synthesis and biological evaluation of a newer series of pyrazolo[1,5-a]pyrimidine analogues as potential anti-tubercular agents. Bioorg Chem 2019; 87:240-251. [PMID: 30908967 DOI: 10.1016/j.bioorg.2019.02.044] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/23/2019] [Accepted: 02/20/2019] [Indexed: 11/16/2022]
Abstract
In-depth study of structure-based drug designing can provide vital leads for the development of novel, clinically active molecules. In this present study, twenty six novel pyrazolo[1,5-a]pyrimidine analogues (6a-6z) were designed using molecular docking studies. The designed molecules were synthesized in good yields. Structural elucidation of the synthesized molecules was carried out using IR, MS, 1H NMR and 13C NMR spectroscopy. All the synthesized compounds were evaluated for their in-vitro anti-tubercular activity against H37Rv strain by Alamar Blue assay method. Most of the synthesized compounds displayed potent anti-tubercular activities. Amongst all the tested compounds 6p, 6g, 6n and 6h exhibited promising anti-tubercular activity. Further, these potent compounds were gauged for MDR-TB, XDR-TB and cytotoxic study. None of these compounds exhibited potent cytotoxicity. Stability of protein ligand complex was further evaluated by molecular dynamics simulation for 10 ns. All these results indicate that the synthesized compounds could be potential leads for further development of new potent anti-tubercular agents.
Collapse
Affiliation(s)
- Palmi Modi
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Navrangpura, Ahmedabad, 380009 Gujarat, India; Department of Pharmacy, Dharmsinh Desai University, Nadiad, 387001 Gujarat, India; Department of Pharmaceutical Chemistry, L. J. Institute of Pharmacy, Ahmedabad, 382210 Gujarat, India
| | - Shivani Patel
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Navrangpura, Ahmedabad, 380009 Gujarat, India; Division of Biological and Life Sciences, Ahmedabad University, Ahmedabad, 380009 Gujarat, India
| | - Mahesh Chhabria
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Navrangpura, Ahmedabad, 380009 Gujarat, India.
| |
Collapse
|
5
|
Rote RV, Shelar DP, Patil SR, Jachak MN. A Convenient Synthesis of New Pyrazolo[4,3-d]pyrimidines and Their Fused Heterocycles. J Heterocycl Chem 2013. [DOI: 10.1002/jhet.2006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ramhari V. Rote
- Department of Chemistry, Organic Chemistry Research Centre, K. T. H. M. College; University of Pune; Gangapur Road Nashik 422002 Maharashtra India
| | - Deepak P. Shelar
- Department of Chemistry, Organic Chemistry Research Centre, K. T. H. M. College; University of Pune; Gangapur Road Nashik 422002 Maharashtra India
| | - Sandeep R. Patil
- Department of Chemistry, Organic Chemistry Research Centre, K. T. H. M. College; University of Pune; Gangapur Road Nashik 422002 Maharashtra India
| | - Madhukar N. Jachak
- Department of Chemistry, Organic Chemistry Research Centre, K. T. H. M. College; University of Pune; Gangapur Road Nashik 422002 Maharashtra India
| |
Collapse
|
6
|
Baraldi PG, Preti D, Borea PA, Varani K. Medicinal Chemistry of A3 Adenosine Receptor Modulators: Pharmacological Activities and Therapeutic Implications. J Med Chem 2012; 55:5676-703. [DOI: 10.1021/jm300087j] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Pier Giovanni Baraldi
- Dipartimento
di Scienze Farmaceutiche and ‡Dipartimento di Medicina Clinica e Sperimentale-Sezione
di Farmacologia, Università di Ferrara, 44121 Ferrara, Italy
| | - Delia Preti
- Dipartimento
di Scienze Farmaceutiche and ‡Dipartimento di Medicina Clinica e Sperimentale-Sezione
di Farmacologia, Università di Ferrara, 44121 Ferrara, Italy
| | - Pier Andrea Borea
- Dipartimento
di Scienze Farmaceutiche and ‡Dipartimento di Medicina Clinica e Sperimentale-Sezione
di Farmacologia, Università di Ferrara, 44121 Ferrara, Italy
| | - Katia Varani
- Dipartimento
di Scienze Farmaceutiche and ‡Dipartimento di Medicina Clinica e Sperimentale-Sezione
di Farmacologia, Università di Ferrara, 44121 Ferrara, Italy
| |
Collapse
|
7
|
Dolzhenko AV, Tan GK, Dolzhenko AV, Koh LL, Pastorin G. 8-Methyl-2-[4-(trifluoro-meth-yl)phen-yl]-8H-pyrazolo-[4,3-e][1,2,4]triazolo[1,5-c]pyrimidin-5-amine methanol disolvate. Acta Crystallogr Sect E Struct Rep Online 2010; 66:o1835-6. [PMID: 21588038 PMCID: PMC3007048 DOI: 10.1107/s1600536810024591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 06/23/2010] [Indexed: 11/10/2022]
Abstract
In the title compound, C(14)H(10)F(3)N(7)·2CH(4)O, the heterocyclic ring system is essentially planar (r.m.s. deviation = 0.009 Å) and makes a dihedral angle of 6.91 (8)° with the attached benzene ring. In the crystal, the main mol-ecules form centrosymmetric R(2) (2)(8) dimers via pairs of N-H⋯N hydrogen bonds between the amino groups and pyrimidine N atoms. One of the independent methanol mol-ecules and its inversion equivalent are linked to the dimers via O-H⋯N and N-H⋯O hydrogen bonds, forming R(4) (4)(16) graph-set motifs. The dimers along with the hydrogen-bonded methanol mol-ecules are stacked along the a axis, with π-π inter-actions between the pyrazole and triazole rings [centroid-centroid distance = 3.4953 (10) Å].
Collapse
|
8
|
Katritch V, Jaakola VP, Lane JR, Lin J, Ijzerman AP, Yeager M, Kufareva I, Stevens RC, Abagyan R. Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists. J Med Chem 2010; 53:1799-809. [PMID: 20095623 DOI: 10.1021/jm901647p] [Citation(s) in RCA: 200] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The recent progress in crystallography of G-protein coupled receptors opens an unprecedented venue for structure-based GPCR drug discovery. To test efficiency of the structure-based approach, we performed molecular docking and virtual ligand screening (VLS) of more than 4 million commercially available "drug-like" and ''lead-like'' compounds against the A(2A)AR 2.6 A resolution crystal structure. Out of 56 high ranking compounds tested in A(2A)AR binding assays, 23 showed affinities under 10 microM, 11 of those had sub-microM affinities and two compounds had affinities under 60 nM. The identified hits represent at least 9 different chemical scaffolds and are characterized by very high ligand efficiency (0.3-0.5 kcal/mol per heavy atom). Significant A(2A)AR antagonist activities were confirmed for 10 out of 13 ligands tested in functional assays. High success rate, novelty, and diversity of the chemical scaffolds and strong ligand efficiency of the A(2A)AR antagonists identified in this study suggest practical applicability of receptor-based VLS in GPCR drug discovery.
Collapse
Affiliation(s)
- Vsevolod Katritch
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Katritch V, Rueda M, Lam PCH, Yeager M, Abagyan R. GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex. Proteins 2010; 78:197-211. [PMID: 20063437 DOI: 10.1002/prot.22507] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Proteins of the G-protein coupled receptor (GPCR) family present numerous attractive targets for rational drug design, but also a formidable challenge for identification and conformational modeling of their 3D structure. A recently performed assessment of blind predictions of adenosine A2a receptor (AA2AR) structure in complex with ZM241385 (ZMA) antagonist provided a first example of unbiased evaluation of the current modeling algorithms on a GPCR target with approximately 30% sequence identity to the closest structural template. Several of the 29 groups participating in this assessment exercise (Michino et al., doi: 10.1038/nrd2877) successfully predicted the overall position of the ligand ZMA in the AA2AR ligand binding pocket, however models from only three groups captured more than 40% the ligand-receptor contacts. Here we describe two of these top performing approaches, in which all-atom models of the AA2AR were generated by homology modeling followed by ligand guided backbone ensemble receptor optimization (LiBERO). The resulting AA2AR-ZMA models, along with the best models from other groups are assessed here for their vitual ligand screening (VLS) performance on a large set of GPCR ligands. We show that ligand guided optimization was critical for improvement of both ligand-receptor contacts and VLS performance as compared to the initial raw homology models. The best blindly predicted models performed on par with the crystal structure of AA2AR in selecting known antagonists from decoys, as well as from antagonists for other adenosine subtypes and AA2AR agonists. These results suggest that despite certain inaccuracies, the optimized homology models can be useful in the drug discovery process.
Collapse
Affiliation(s)
- Vsevolod Katritch
- Molsoft LLC, 3366 N. Torrey Pines Court, La Jolla, California 92037, USA
| | | | | | | | | |
Collapse
|
10
|
|
11
|
Jacobson KA, Klutz AM, Tosh DK, Ivanov AA, Preti D, Baraldi PG. Medicinal chemistry of the A3 adenosine receptor: agonists, antagonists, and receptor engineering. Handb Exp Pharmacol 2009:123-59. [PMID: 19639281 PMCID: PMC3413728 DOI: 10.1007/978-3-540-89615-9_5] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A(3) adenosine receptor (A(3)AR) ligands have been modified to optimize their interaction with the A(3)AR. Most of these modifications have been made to the N(6) and C2 positions of adenine as well as the ribose moiety, and using a combination of these substitutions leads to the most efficacious, selective, and potent ligands. A(3)AR agonists such as IB-MECA and Cl-IB-MECA are now advancing into Phase II clinical trials for treatments targeting diseases such as cancer, arthritis, and psoriasis. Also, a wide number of compounds exerting high potency and selectivity in antagonizing the human (h)A(3)AR have been discovered. These molecules are generally characterized by a notable structural diversity, taking into account that aromatic nitrogen-containing monocyclic (thiazoles and thiadiazoles), bicyclic (isoquinoline, quinozalines, (aza)adenines), tricyclic systems (pyrazoloquinolines, triazoloquinoxalines, pyrazolotriazolopyrimidines, triazolopurines, tricyclic xanthines) and nucleoside derivatives have been identified as potent and selective A(3)AR antagonists. Probably due to the "enigmatic" physiological role of A(3)AR, whose activation may produce opposite effects (for example, concerning tissue protection in inflammatory and cancer cells) and may produce effects that are species dependent, only a few molecules have reached preclinical investigation. Indeed, the most advanced A(3)AR antagonists remain in preclinical testing. Among the antagonists described above, compound OT-7999 is expected to enter clinical trials for the treatment of glaucoma, while several thiazole derivatives are in development as antiallergic, antiasthmatic and/or antiinflammatory drugs.
Collapse
Affiliation(s)
- Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0810, USA.
| | | | | | | | | | | |
Collapse
|
12
|
Michielan L, Bacilieri M, Schiesaro A, Bolcato C, Pastorin G, Spalluto G, Cacciari B, Klotz KN, Kaseda C, Moro S. Linear and nonlinear 3D-QSAR approaches in tandem with ligand-based homology modeling as a computational strategy to depict the pyrazolo-triazolo-pyrimidine antagonists binding site of the human adenosine A2A receptor. J Chem Inf Model 2008; 48:350-63. [PMID: 18215030 DOI: 10.1021/ci700300w] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The integration of ligand- and structure-based strategies might sensitively increase the success of drug discovery process. We have recently described the application of Molecular Electrostatic Potential autocorrelated vectors (autoMEPs) in generating both linear (Partial Least-Square, PLS) and nonlinear (Response Surface Analysis, RSA) 3D-QSAR models to quantitatively predict the binding affinity of human adenosine A3 receptor antagonists. Moreover, we have also reported a novel GPCR modeling approach, called Ligand-Based Homology Modeling (LBHM), as a tool to simulate the conformational changes of the receptor induced by ligand binding. In the present study, the application of both linear and nonlinear 3D-QSAR methods and LBHM computational techniques has been used to depict the hypothetical antagonist binding site of the human adenosine A2A receptor. In particular, a collection of 127 known human A2A antagonists has been utilized to derive two 3D-QSAR models (autoMEPs/PLS&RSA). In parallel, using a rhodopsin-driven homology modeling approach, we have built a model of the human adenosine A2A receptor. Finally, 3D-QSAR and LBHM strategies have been utilized to predict the binding affinity of five new human A2A pyrazolo-triazolo-pyrimidine antagonists finding a good agreement between the theoretical and the experimental predictions.
Collapse
Affiliation(s)
- Lisa Michielan
- Molecular Modeling Section, Dipartimento di Scienze Farmaceutiche, Università di Padova, via Marzolo 5, I-35131 Padova, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|