1
|
Chatterjee A, Jayaprakasan M, Chakrabarty AK, Lakkaniga NR, Bhatt BN, Banerjee D, Narwaria A, Katiyar CK, Dubey SK. Comprehensive insights into rheumatoid arthritis: Pathophysiology, current therapies and herbal alternatives for effective disease management. Phytother Res 2024. [PMID: 38522945 DOI: 10.1002/ptr.8187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/14/2024] [Accepted: 03/01/2024] [Indexed: 03/26/2024]
Abstract
Rheumatoid arthritis is a chronic autoimmune inflammatory disease characterized by immune response overexpression, causing pain and swelling in the synovial joints. This condition is caused by auto-reactive antibodies that attack self-antigens due to their incapacity to distinguish between self and foreign molecules. Dysregulated activity within numerous signalling and immunological pathways supports the disease's development and progression, elevating its complexity. While current treatments provide some alleviation, their effectiveness is accompanied by a variety of adverse effects that are inherent in conventional medications. As a result, there is a deep-rooted necessity to investigate alternate therapeutic strategies capable of neutralizing these disadvantages. Medicinal herbs display a variety of potent bioactive phytochemicals that are effective in the complementary management of disease, thus generating an enormous potency for the researchers to delve deep into the development of novel phytomedicine against autoimmune diseases, although additional evidence and understanding are required in terms of their efficacy and pharmacodynamic mechanisms. This literature-based review highlights the dysregulation of immune tolerance in rheumatoid arthritis, analyses the pathophysiology, elucidates relevant signalling pathways involved, evaluates present and future therapy options and underscores the therapeutic attributes of a diverse array of medicinal herbs in addressing this severe disease.
Collapse
Affiliation(s)
- Amrita Chatterjee
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines), Dhanbad, India
| | - Monisha Jayaprakasan
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines), Dhanbad, India
| | | | - Naga Rajiv Lakkaniga
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines), Dhanbad, India
| | | | | | | | | | | |
Collapse
|
2
|
Lakkaniga NR, Wang Z, Xiao Y, Kharbanda A, Lan L, Li HY. Revisiting Aurora Kinase B: A promising therapeutic target for cancer therapy. Med Res Rev 2024; 44:686-706. [PMID: 37983866 DOI: 10.1002/med.21994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 03/28/2023] [Accepted: 10/29/2023] [Indexed: 11/22/2023]
Abstract
Cancer continues to be a major health concern globally, although the advent of targeted therapy has revolutionized treatment options. Aurora Kinase B is a serine-threonine kinase that has been explored as an oncology therapeutic target for more than two decades. Aurora Kinase B inhibitors show promising biological results in in-vitro and in-vivo experiments. However, there are no inhibitors approved yet for clinical use, primarily because of the side effects associated with Aurora B inhibitors. Several studies demonstrate that Aurora B inhibitors show excellent synergy with various chemotherapeutic agents, radiation therapy, and targeted therapies. This makes it an excellent choice as an adjuvant therapy to first-line therapies, which greatly improves the therapeutic window and side effect profile. Recent studies indicate the role of Aurora B in some deadly cancers with limited therapeutic options, like triple-negative breast cancer and glioblastoma. Herein, we review the latest developments in Aurora Kinase B targeted research, with emphasis on its potential as an adjuvant therapy and its role in some of the most difficult-to-treat cancers.
Collapse
Affiliation(s)
- Naga Rajiv Lakkaniga
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines), Dhanbad, India
| | - Zhengyu Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Yao Xiao
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Anupreet Kharbanda
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| |
Collapse
|
3
|
Acharya B, Saha D, Armstrong D, Jabali B, Hanafi M, Herrera-Rueda A, Lakkaniga NR, Frett B. Kinase inhibitor macrocycles: a perspective on limiting conformational flexibility when targeting the kinome with small molecules. RSC Med Chem 2024; 15:399-415. [PMID: 38389874 PMCID: PMC10880908 DOI: 10.1039/d3md00457k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/10/2023] [Indexed: 02/24/2024] Open
Abstract
Methods utilized for drug discovery and development within the kinome have rapidly evolved since the approval of imatinib, the first small molecule kinase inhibitor. Macrocycles have received increasing interest as a technique to improve kinase inhibitor drug properties evident by the FDA approvals of lorlatinib, pacritinib, and repotrectinib. Compared to their acyclic counterparts, macrocycles can possess improved pharmacodynamic and pharmacokinetic properties. This review highlights clinical success stories when implementing macrocycles in kinase-based drug discovery and showcases that macrocyclization is a clinically validated drug discovery strategy when targeting the kinome.
Collapse
Affiliation(s)
- Baku Acharya
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
| | - Debasmita Saha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
- Conrad Prebys Centre for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute San Diego CA USA
| | - Daniel Armstrong
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
| | - Baha'a Jabali
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
| | - Maha Hanafi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University Cairo 11526 Egypt
| | - Alan Herrera-Rueda
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
| | - Naga Rajiv Lakkaniga
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR USA
| |
Collapse
|
4
|
Sharma PD, Rallapalli S, Lakkaniga NR. An innovative approach for predicting pandemic hotspots in complex wastewater networks using graph theory coupled with fuzzy logic. Stoch Environ Res Risk Assess 2023; 37:1-18. [PMID: 37362844 PMCID: PMC10198017 DOI: 10.1007/s00477-023-02468-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/07/2023] [Indexed: 06/28/2023]
Abstract
Early prediction of COVID-19 infected communities (potential hotspots) is essential to limit the spread of virus. Diagnostic testing has limitations in big populations because it cannot deliver information at a fast enough rate to stop the spread in its early phases. Wastewater based epidemiology (WBE) experiments showed promising results for brisk detection of 'SARS CoV-2' RNA in urban wastewater. However, a systematic and targeted approach to track COVID-19 virus in the complex wastewater networks at a community level is lacking. This research combines graph network (GN) theory with fuzzy logic to determine the chances of a specific community being a COVID-19 hotspot in a wastewater network. To detect 'SARS-CoV-2' RNA, GN divides wastewater network into communities and fuzzy logic-based inference system is used to identify targeted communities. For the propose of tracking, 4000 sample cases from Minnesota (USA) were tested based on various contributing factors. With a probability score of greater than 0.8, 42% of cases were likely to be designated as COVID-19 hotspots based on multiple demographic characteristics. The research enhances the conventional WBE approach through two novel aspects, viz. (1) by integrating graph theory with fuzzy logic for quick prediction of potential hotspot along with its likelihood percentage in a wastewater network, and (2) incorporating the uncertainty associated with COVID-19 contributing factors using fuzzy membership functions. The targeted approach allows for rapid testing and implementation of vaccination campaigns in potential hotspots. Consequently, governmental bodies can be well prepared to check future pandemics and variant spreading in a more planned manner. Supplementary Information The online version contains supplementary material available at 10.1007/s00477-023-02468-3.
Collapse
Affiliation(s)
- Puru Dutt Sharma
- Department of Civil Engineering, Birla Institute of Technology and Science, Pilani, Rajasthan India
| | - Srinivas Rallapalli
- Department of Civil Engineering, Birla Institute of Technology and Science, Pilani, Rajasthan India
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, Twin Cities, Minneapolis, MN USA
| | - Naga Rajiv Lakkaniga
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand India
| |
Collapse
|
5
|
Rohmetra H, Raghunath N, Narang P, Chamola V, Guizani M, Lakkaniga NR. AI-enabled remote monitoring of vital signs for COVID-19: methods, prospects and challenges. Computing 2023; 105. [PMCID: PMC8006120 DOI: 10.1007/s00607-021-00937-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The COVID-19 pandemic has overwhelmed the existing healthcare infrastructure in many parts of the world. Healthcare professionals are not only over-burdened but also at a high risk of nosocomial transmission from COVID-19 patients. Screening and monitoring the health of a large number of susceptible or infected individuals is a challenging task. Although professional medical attention and hospitalization are necessary for high-risk COVID-19 patients, home isolation is an effective strategy for low and medium risk patients as well as for those who are at risk of infection and have been quarantined. However, this necessitates effective techniques for remotely monitoring the patients’ symptoms. Recent advances in Machine Learning (ML) and Deep Learning (DL) have strengthened the power of imaging techniques and can be used to remotely perform several tasks that previously required the physical presence of a medical professional. In this work, we study the prospects of vital signs monitoring for COVID-19 infected as well as quarantined individuals by using DL and image/signal-processing techniques, many of which can be deployed using simple cameras and sensors available on a smartphone or a personal computer, without the need of specialized equipment. We demonstrate the potential of ML-enabled workflows for several vital signs such as heart and respiratory rates, cough, blood pressure, and oxygen saturation. We also discuss the challenges involved in implementing ML-enabled techniques.
Collapse
Affiliation(s)
- Honnesh Rohmetra
- Department of CSIS, Birla Institute of Technology and Science, Pilani, Pilani, Rajasthan India
| | - Navaneeth Raghunath
- Department of CSIS, Birla Institute of Technology and Science, Pilani, Pilani, Rajasthan India
| | - Pratik Narang
- Department of CSIS, Birla Institute of Technology and Science, Pilani, Pilani, Rajasthan India
| | - Vinay Chamola
- Department of EEE & APPCAIR, Birla Institute of Technology and Science, Pilani, Pilani, Rajasthan India
| | | | - Naga Rajiv Lakkaniga
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, USA
- SmartBio Labs, Chennai, India
| |
Collapse
|
6
|
Acharya B, Saha D, Armstrong D, Lakkaniga NR, Frett B. FLT3 inhibitors for acute myeloid leukemia: successes, defeats, and emerging paradigms. RSC Med Chem 2022; 13:798-816. [PMID: 35923716 PMCID: PMC9298189 DOI: 10.1039/d2md00067a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/21/2022] [Indexed: 09/10/2023] Open
Abstract
FLT3 mutations are one of the most common genetic aberrations found in nearly 30% of acute myeloid leukemias (AML). The mutations are associated with poor prognosis despite advances in the understanding of the biological mechanisms of AML. Numerous small molecule FLT3 inhibitors have been developed in an effort to combat AML. Even with the development of these inhibitors, the five-year overall survival for newly diagnosed AML is less than 30%. In 2017, midostaurin received FDA approval to treat AML, which was the first approved FLT3 inhibitor in the U.S. and Europe. Following, gilteritinib received FDA approval in 2018 and in 2019 quizartinib received approval in Japan. This review parallels these clinical success stories along with other pre-clinical and clinical investigations of FLT3 inhibitors.
Collapse
Affiliation(s)
- Baku Acharya
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR 72205 USA
| | - Debasmita Saha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR 72205 USA
| | - Daniel Armstrong
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR 72205 USA
| | - Naga Rajiv Lakkaniga
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad Jharkhand 826004 India
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences Little Rock AR 72205 USA
| |
Collapse
|
7
|
Zhang L, Moccia M, Briggs DC, Bharate JB, Lakkaniga NR, Knowles P, Yan W, Tran P, Kharbanda A, Wang X, Leung YK, Frett B, Santoro M, McDonald NQ, Carlomagno F, Li HY. Discovery of N-Trisubstituted Pyrimidine Derivatives as Type I RET and RET Gatekeeper Mutant Inhibitors with a Novel Kinase Binding Pose. J Med Chem 2022; 65:1536-1551. [PMID: 35081714 PMCID: PMC10536133 DOI: 10.1021/acs.jmedchem.1c01280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Mutations of the rearranged during transfection (RET) kinase are frequently reported in cancer, which make it as an attractive therapeutic target. Herein, we discovered a series of N-trisubstituted pyrimidine derivatives as potent inhibitors for both wild-type (wt) RET and RETV804M, which is a resistant mutant for several FDA-approved inhibitors. The X-ray structure of a representative inhibitor with RET revealed that the compound binds in a unique pose that bifurcates beneath the P-loop and confirmed the compound as a type I inhibitor. Through the structure-activity relationship (SAR) study, compound 20 was identified as a lead compound, showing potent inhibition of both RET and RETV804M. Additionally, compound 20 displayed potent antiproliferative activity of CCDC6-RET-driven LC-2/ad cells. Analysis of RET phosphorylation indicated that biological activity was mediated by RET inhibition. Collectively, N-trisubstituted pyrimidine derivatives could serve as scaffolds for the discovery and development of potent inhibitors of type I RET and its gatekeeper mutant for the treatment of RET-driven cancers.
Collapse
Affiliation(s)
- Lingtian Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Marialuisa Moccia
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", 80131 Napoli, Italia
| | - David C Briggs
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Jaideep B Bharate
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Naga Rajiv Lakkaniga
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Phillip Knowles
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Wei Yan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Phuc Tran
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Anupreet Kharbanda
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Xiuqi Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Yuet-Kin Leung
- Department of Pharmacology & Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Massimo Santoro
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", 80131 Napoli, Italia
| | - Neil Q McDonald
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, U.K
| | - Francesca Carlomagno
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", 80131 Napoli, Italia
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR, 80131 Napoli, Italia
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| |
Collapse
|
8
|
Saha D, Ryan KR, Lakkaniga NR, Acharya B, Garcia NG, Smith EL, Frett B. Targeting Rearranged during Transfection in Cancer: A Perspective on Small-Molecule Inhibitors and Their Clinical Development. J Med Chem 2021; 64:11747-11773. [PMID: 34402300 DOI: 10.1021/acs.jmedchem.0c02167] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rearranged during transfection (RET) is a receptor tyrosine kinase essential for the normal development and maturation of a diverse range of tissues. Aberrant RET signaling in cancers, due to RET mutations, gene fusions, and overexpression, results in the activation of downstream pathways promoting survival, growth, and metastasis. Pharmacological manipulation of RET is effective in treating RET-driven cancers, and efforts toward developing RET-specific therapies have increased over the last 5 years. In 2020, RET-selective inhibitors pralsetinib and selpercatinib achieved clinical approval, which marked the first approvals for kinase inhibitors specifically developed to target the RET oncoprotein. This Perspective discusses current development and clinical applications for RET precision medicine by providing an overview of the incremental improvement of kinase inhibitors for use in RET-driven malignancies.
Collapse
Affiliation(s)
- Debasmita Saha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 United States
| | - Katie Rose Ryan
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 United States
| | - Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 United States
| | - Baku Acharya
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 United States
| | - Noemi Garcia Garcia
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 United States
| | - Erica Lane Smith
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 United States
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205 United States
| |
Collapse
|
9
|
Moccia M, Yang D, Lakkaniga NR, Frett B, McConnell N, Zhang L, Brescia A, Federico G, Zhang L, Salerno P, Santoro M, Li HY, Carlomagno F. Targeted activity of the small molecule kinase inhibitor Pz-1 towards RET and TRK kinases. Sci Rep 2021; 11:16103. [PMID: 34373541 PMCID: PMC8352932 DOI: 10.1038/s41598-021-95612-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 07/20/2021] [Indexed: 11/09/2022] Open
Abstract
We have recently described Pz-1, a benzimidazole-based type-2 RET and VEGFR2 inhibitor. Based on a kinome scan, here we show that Pz-1 is also a potent (IC50 < 1 nM) TRKA/B/C inhibitor. Pz-1 potently inhibited proliferation of human cancer cells carrying either RET- or TRKA oncoproteins (IC50 ~ 1 nM), with a negligible effect against RET- and TRKA-negative cells. By testing mutations, known to mediate resistance to other compounds, RET G810R/S, but not L730I/V, E732K, V738A and Y806N, showed some degree of resistance to Pz-1. In the case of TRKA, G595R and F589L, but not G667C, showed some degree of resistance. In xenograft models, orally administered Pz-1 almost completely inhibited RET- and TRKA-mutant tumours at 1-3 mg/kg/day but showed a reduced effect on RET/TRKA-negative cancer models. The activity, albeit reduced, on RET/TRKA-negative tumours may be justified by VEGFR2 inhibition. Tumours induced by NIH3T3 cells transfected by RET G810R and TRKA G595R featured resistance to Pz-1, demonstrating that RET or TRKA inhibition is critical for its anti-tumourigenic effect. In conclusion, Pz-1 represents a new powerful kinase inhibitor with distinct activity towards cancers induced by oncogenic RET and TRKA variants, including some mutants displaying resistance to other drugs.
Collapse
Affiliation(s)
- Marialuisa Moccia
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Di Napoli "Federico II", Via S. Pansini 5, 80131, Naples, Italy
| | - Donglin Yang
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Di Napoli "Federico II", Via S. Pansini 5, 80131, Naples, Italy
| | - Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.,Synactix Pharmaceuticals, Inc., Tucson, AZ, 85718, USA
| | - Nicholas McConnell
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Lingtian Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Annalisa Brescia
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Di Napoli "Federico II", Via S. Pansini 5, 80131, Naples, Italy
| | - Giorgia Federico
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Di Napoli "Federico II", Via S. Pansini 5, 80131, Naples, Italy
| | - Lingzhi Zhang
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Di Napoli "Federico II", Via S. Pansini 5, 80131, Naples, Italy
| | - Paolo Salerno
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Di Napoli "Federico II", Via S. Pansini 5, 80131, Naples, Italy
| | - Massimo Santoro
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Di Napoli "Federico II", Via S. Pansini 5, 80131, Naples, Italy
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA. .,Synactix Pharmaceuticals, Inc., Tucson, AZ, 85718, USA.
| | - Francesca Carlomagno
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Di Napoli "Federico II", Via S. Pansini 5, 80131, Naples, Italy. .,Istituto di Endocrinologia ed Oncologia Sperimentale del CNR, 80131, Naples, Italy.
| |
Collapse
|
10
|
Bowroju SK, Penthala NR, Lakkaniga NR, Balasubramaniam M, Ayyadevara S, Shmookler Reis RJ, Crooks PA. Novel hydroxybenzylamine-deoxyvasicinone hybrids as anticholinesterase therapeutics for Alzheimer's disease. Bioorg Med Chem 2021; 45:116311. [PMID: 34304133 DOI: 10.1016/j.bmc.2021.116311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 12/31/2022]
Abstract
A series of novel 2-hydroxybenzylamine-deoxyvasicinone hybrid analogs (8a-8n) have been synthesized and evaluated as inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), and as inhibitors of amyloid peptide (Aβ1-42) aggregation, for treatment of Alzheimer's disease (AD). These dual acting compounds exhibited good AChE inhibitory activities ranging from 0.34 to 6.35 µM. Analogs8g and 8n were found to be the most potent AChE inhibitors in the series with IC50values of 0.38 µM and 0.34 µM, respectively. All the analogs (8a-8n) exhibited weak BuChE inhibitory activities ranging from 14.60 to 21.65 µM. Analogs8g and 8n exhibited BuChE with IC50values of 15.38 µM and 14.60 µM, respectively, demonstrating that these analogs were greater than 40-fold more selective for inhibition of AChE over BuChE. Additionally, compounds8g and 8n were also found to be the best inhibitors of self-induced Aβ1-42 peptide aggregation with IC50values of 3.91 µM and 3.22 µM, respectively; 8g and 8n also inhibited AChE-induced Aβ1-42 peptide aggregation by 68.7% and 72.6%, respectively. Kinetic analysis and molecular docking studies indicate that analogs 8g and 8n bind to a new allosteric pocket (site B) on AChE. In addition, the observed inhibition of AChE-induced Aβ1-42 peptide aggregation by 8n is likely due to allosteric inhibition of the binding of this peptide at the CAS site on AChE. Overall, these results indicate that 8g and 8n are examples of dual-acting lead compounds for the development of highly effective anti-AD drugs.
Collapse
Affiliation(s)
- Suresh K Bowroju
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Narsimha R Penthala
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Naga Rajiv Lakkaniga
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | | | - Srinivas Ayyadevara
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Robert J Shmookler Reis
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, United States; BioInformatics Program, University of Arkansas for Medical Sciences and University of Arkansas at Little Rock, Little Rock, AR 72205, United States
| | - Peter A Crooks
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States.
| |
Collapse
|
11
|
Saha D, Ryan KR, Lakkaniga NR, Smith EL, Frett B. Pyrazoloadenine Inhibitors of the RET Lung Cancer Oncoprotein Discovered by a Fragment Optimization Approach. ChemMedChem 2021; 16:1605-1608. [PMID: 33559353 PMCID: PMC9969764 DOI: 10.1002/cmdc.202100013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/01/2021] [Indexed: 12/24/2022]
Abstract
A fragment-based drug-discovery approach was used on a pyrazoloadenine fragment library to uncover new molecules that target the RET (REarranged during Transfection) oncoprotein, which is a driver oncoprotein in ∼2 % of non-small-cell lung cancers. The fragment library was screened against the RET kinase and LC-2/ad (RET-driven), KM-12 (TRKA-driven matched control) and A549 (cytotoxic control) cells to identify selective scaffolds that could inhibit RET-driven growth. An unsubstituted pyrazoloadenine fragment was found to be active on RET in a biochemical assay, but reduced cell viability in non-RET-driven cell lines (EC50 =1 and 3 μM, respectively). To increase selectivity for RET, the pyrazoloadenine was modeled in the RET active site, and two domains were identified that were probed with pyrazoloadenine fragment derivatives to improve RET affinity. Scaffolds at each domain were merged to generate a novel lead compound, 8 p, which exhibited improved activity and selectivity for the RET oncoprotein (A549 EC50 =5.92 μM, LC-2/ad EC50 =0.016 μM, RET IC50 =0.000326 μM).
Collapse
Affiliation(s)
- Debasmita Saha
- Department of Pharmaceutical Sciences, College of Pharm
acy, University of Arkansas for Medical Sciences, Little Rock, AR USA
| | - Katie Rose Ryan
- Department of Biochemistry and Molecular Biology, College
of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR USA
| | - Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharm
acy, University of Arkansas for Medical Sciences, Little Rock, AR USA,SmartBio Labs, Chennai, India
| | - Erica Lane Smith
- Department of Pharmaceutical Sciences, College of Pharm
acy, University of Arkansas for Medical Sciences, Little Rock, AR USA
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharm
acy, University of Arkansas for Medical Sciences, Little Rock, AR USA
| |
Collapse
|
12
|
Lakkaniga NR, Gunaganti N, Zhang L, Belachew B, Frett B, Leung YK, Li HY. Pyrrolo[2,3-d]pyrimidine derivatives as inhibitors of RET: Design, synthesis and biological evaluation. Eur J Med Chem 2020; 206:112691. [PMID: 32823007 PMCID: PMC10536156 DOI: 10.1016/j.ejmech.2020.112691] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 12/17/2022]
Abstract
Gene fusions and point mutations of RET kinase are crucial for driving thoracic cancers, including thyroid cancer and non-small cell lung cancer. Various scaffolds based on different heterocycles have been synthesized and evaluated as RET inhibitors. In this work, we investigate pyrrolo[2,3-d]pyrimidine derivatives for inhibition of RET-wt, drug resistant mutant RET V804M and RET gene fusion driven cell lines. Several compounds were synthesized and the structure activity relationship was extensively studied to optimize the scaffold. Thieno[2,3-d]pyrimidine, a bioisostere of pyrrolo[2,3-d]pyrimidine, was also explored for the effect on RET inhibition. We identified a lead compound, 59, which shows low nanomolar potency against RET-wt and RET V804M. Further 59 shows growth inhibition of LC-2/ad cells which RET-CCDC6 driven. We also determined that 59 is a type 2 inhibitor of RET and demonstrated its ability to inhibit migration of tumor cells. Based on computational studies, we proposed a binding pose of 59 in RET pocket and have quantified the contributions of individual residues for its binding. Together, 59 is an important lead compound which needs further evaluation in biological studies.
Collapse
Affiliation(s)
- Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Naresh Gunaganti
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Lingtian Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Binyam Belachew
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yuet-Kin Leung
- Department of Pharmacology & Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| |
Collapse
|
13
|
Yan W, Lakkaniga NR, Carlomagno F, Santoro M, McDonald NQ, Lv F, Gunaganti N, Frett B, Li HY. Correction to Insights into Current Tropomyosin Receptor Kinase (TRK) Inhibitors: Development and Clinical Application. J Med Chem 2020; 63:10089. [DOI: 10.1021/acs.jmedchem.0c01351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
14
|
Lakkaniga NR, Zhang L, Belachew B, Gunaganti N, Frett B, Li HY. Discovery of SP-96, the first non-ATP-competitive Aurora Kinase B inhibitor, for reduced myelosuppression. Eur J Med Chem 2020; 203:112589. [PMID: 32717530 DOI: 10.1016/j.ejmech.2020.112589] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/01/2020] [Accepted: 06/08/2020] [Indexed: 12/22/2022]
Abstract
Aurora Kinase B is a serine-threonine kinase known to be overexpressed in several cancers, with no inhibitors approved for clinical use. Herein, we present the discovery and optimization of a series of novel quinazoline-based Aurora Kinase B inhibitors. The lead inhibitor SP-96 shows sub-nanomolar potency in Aurora B enzymatic assays (IC50 = 0.316 ± 0.031 nM). We identified the important pharmacophore features resulting in selectivity against receptor tyrosine kinases. Particularly, SP-96 shows >2000 fold selectivity against FLT3 and KIT which is important for normal hematopoiesis. This could diminish the adverse effect of neutropenia reported in the clinical trials of the Aurora B inhibitor Barasertib, which inhibits FLT3 and KIT in addition to Aurora B. Enzyme kinetics of SP-96 shows non-ATP-competitive inhibition which makes it a first-in-class inhibitor. Further, SP-96 shows selective growth inhibition in NCI60 screening, including inhibition of MDA-MD-468, a Triple Negative Breast Cancer cell line.
Collapse
Affiliation(s)
- Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Lingtian Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Binyam Belachew
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Naresh Gunaganti
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.
| |
Collapse
|
15
|
Moccia M, Frett B, Zhang L, Lakkaniga NR, Briggs DC, Chauhan R, Brescia A, Federico G, Yan W, Santoro M, McDonald NQ, Li HY, Carlomagno F. Bioisosteric Discovery of NPA101.3, a Second-Generation RET/VEGFR2 Inhibitor Optimized for Single-Agent Polypharmacology. J Med Chem 2020; 63:4506-4516. [PMID: 32298114 PMCID: PMC7901654 DOI: 10.1021/acs.jmedchem.9b01336] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
RET receptor tyrosine kinase is a driver oncogene in human cancer. We recently identified the clinical drug candidate Pz-1, which targets RET and VEGFR2. A key in vivo metabolite of Pz-1 is its less active demethylated pyrazole analogue. Using bioisosteric substitution methods, here, we report the identification of NPA101.3, lacking the structural liability for demethylation. NPA101.3 showed a selective inhibitory profile and an inhibitory concentration 50 (IC50) of <0.003 μM for both RET and VEGFR2. NPA101.3 inhibited phosphorylation of all tested RET oncoproteins as well as VEGFR2 and proliferation of cells transformed by RET. Oral administration of NPA101.3 (10 mg/kg/day) completely prevented formation of tumors induced by RET/C634Y-transformed cells, while it weakened, but did not abrogate, formation of tumors induced by a control oncogene (HRAS/G12V). The balanced synchronous inhibition of both RET and VEGFR2, as well the resistance to demethylation, renders NPA101.3 a potential clinical candidate for RET-driven cancers.
Collapse
Affiliation(s)
- Marialuisa Moccia
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", 80131 Napoli, Italy
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States.,Synactix Pharmaceuticals, Inc., Tucson, Arizona 85718, United States
| | - Lingtian Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - David C Briggs
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Rakhee Chauhan
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Annalisa Brescia
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", 80131 Napoli, Italy
| | - Giorgia Federico
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", 80131 Napoli, Italy
| | - Wei Yan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Massimo Santoro
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", 80131 Napoli, Italy
| | - Neil Q McDonald
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London NW1 1AT, U.K.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London WC1E 7HX, U.K
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States.,Synactix Pharmaceuticals, Inc., Tucson, Arizona 85718, United States
| | - Francesca Carlomagno
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", 80131 Napoli, Italy.,Istituto di Endocrinologia ed Oncologia Sperimentale del CNR, 80131 Napoli, Italy
| |
Collapse
|
16
|
Balasubramaniam M, Lakkaniga NR, Dera AA, Fayi MA, Abohashrh M, Ahmad I, Chandramoorthy HC, Nalini G, Rajagopalan P. FCX-146, a potent allosteric inhibitor of Akt kinase in cancer cells: Lead optimization of the second-generation arylidene indanone scaffold. Biotechnol Appl Biochem 2020; 68:82-91. [PMID: 32067263 DOI: 10.1002/bab.1896] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/04/2020] [Indexed: 12/16/2022]
Abstract
Akt, a serine-threonine protein kinase, is regulated by class-I PI3K signaling. Akt regulates a wide variety of cell processes including cell proliferation, survival, and angiogenesis through serine/threonine phosphorylation of downstream targets including mTOR and glycogen-synthase-kinase-3-beta (GSK3β). Targeting cancer-specific overexpression of Akt protein could be an efficient way to control cancer-cell proliferation. However, the ATP-competitive inhibitors are challenged by the highly conserved ATP binding site, and by competition with high cellular concentrations of ATP. We previously developed an allosteric inhibitor, 2-arylidene-4, 7-dimethyl indan-1-one (FXY-1) that showed promising activity against several lung cancer models. In this work, we designed a congeneric series of molecules based on FXY-1 and optimized lead based on computational, in vitro assays. Computational screening followed by enzyme-inhibition and cell-proliferation assays identified a derivative (FCX-146) as a new lead molecule with threefold greater potency than the parent compound. FCX-146 increased apoptosis in HL-60 cells, mediated in part through decreased expression of antiapoptotic Bcl-2 protein and increased levels of Bax-2 and Caspase-3. Molecular-dynamic simulations showed stable binding of FCX-146 to an allosteric (i.e., noncatalytic) pocket in Akt. Together, we propose FCX-146 as a potent second-generation arylidene indanone compound that binds to the allosteric pocket of Akt and potently inhibits its activation.
Collapse
Affiliation(s)
| | - Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ayed A Dera
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Majed Al Fayi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohammed Abohashrh
- Department of Basic Medical Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Harish C Chandramoorthy
- Center for Stem Cell Research and Department of Microbiology & Clinical Parasitology College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Ganesan Nalini
- Department of Chemistry, Pachaiyappas College, Chennai, Tamil Nadu, India
| | - Prasanna Rajagopalan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- Central Research Laboratory, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| |
Collapse
|
17
|
Abstract
Chirality is important in drug discovery because stereoselective drugs can ameliorate therapeutic difficulties including adverse toxicity and poor pharmacokinetic profiles. The human kinome, a major druggable enzyme class has been exploited to treat a wide range of diseases. However, many kinase inhibitors are planar and overlap in chemical space, which leads to selectivity and toxicity issues. By exploring chirality within the kinome, a new iteration of kinase inhibitors is being developed to better utilize the three-dimensional nature of the kinase active site. Exploration into novel chemical space, in turn, will also improve drug solubility and pharmacokinetic profiles. This perspective explores the role of chirality to improve kinome druggability and will serve as a resource for pioneering kinase inhibitor development to address current therapeutic needs.
Collapse
Affiliation(s)
- Debasmita Saha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Anupreet Kharbanda
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Wei Yan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| |
Collapse
|
18
|
Lakkaniga NR, Balasubramaniam M, Zhang S, Frett B, Li HY. Structural Characterization of the Aurora Kinase B "DFG-flip" Using Metadynamics. AAPS J 2019; 22:14. [PMID: 31853739 DOI: 10.1208/s12248-019-0399-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/13/2019] [Indexed: 11/30/2022]
Abstract
Aurora kinase B (AKB), a Ser/Thr kinase that plays a crucial role in mitosis, is overexpressed in several cancers. Clinical inhibitors targeting AKB bind to the active DFG "in" conformation of the kinase. It would be beneficial, however, to understand if AKB is susceptible to type II kinase inhibitors that bind to the inactive, DFG "out" conformation, since type II inhibitors achieve higher kinome selectivity and higher potency in vivo. The DFG "out" conformation of AKB is not yet experimentally determined which makes the design of type II inhibitors exceedingly difficult. An alternate approach is to simulate the DFG "out" conformation from the experimentally determined DFG "in" conformation using atomistic molecular dynamics (MD) simulation. In this work, we employed metadynamics (MTD) approach to simulate the DFG "out" conformation of AKB by choosing the appropriate collective variables. We examined structural changes during the DFG-flip and determined the interactions crucial to stabilize the kinase in active and inactive states. Interestingly, the MTD approach also identified a unique transition state (DFG "up"), which can be targeted by small molecule inhibitors. Structural insights about these conformations is essential for structure-guided design of next-generation AKB inhibitors. This work also emphasizes the usefulness of MTD simulations in predicting macromolecular conformational changes at reduced computational costs.
Collapse
Affiliation(s)
- Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA
| | | | - Shuxing Zhang
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77225, USA
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA.
| |
Collapse
|
19
|
Naresh G, Lakkaniga NR, Kharbanda A, Yan W, Frett B, Li H. Use of Imidazo[1,2‐
a
]pyridine as a Carbonyl Surrogate in a Mannich‐Like, Catalyst Free, One‐Pot Reaction. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801430] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Gunaganti Naresh
- Department of Pharmaceutical Sciences College of Pharmacy University of Arkansas for Medical Sciences 4301 W Markham St. 72205 Little Rock Arkansas USA
| | - Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences College of Pharmacy University of Arkansas for Medical Sciences 4301 W Markham St. 72205 Little Rock Arkansas USA
| | - Anupreet Kharbanda
- Department of Pharmaceutical Sciences College of Pharmacy University of Arkansas for Medical Sciences 4301 W Markham St. 72205 Little Rock Arkansas USA
| | - Wei Yan
- Department of Pharmaceutical Sciences College of Pharmacy University of Arkansas for Medical Sciences 4301 W Markham St. 72205 Little Rock Arkansas USA
| | - Brendan Frett
- Department of Pharmaceutical Sciences College of Pharmacy University of Arkansas for Medical Sciences 4301 W Markham St. 72205 Little Rock Arkansas USA
| | - Hong‐yu Li
- Department of Pharmaceutical Sciences College of Pharmacy University of Arkansas for Medical Sciences 4301 W Markham St. 72205 Little Rock Arkansas USA
| |
Collapse
|
20
|
Gunaganti N, Kharbanda A, Lakkaniga NR, Zhang L, Cooper R, Li HY, Frett B. Catalyst free, C-3 functionalization of imidazo[1,2-a]pyridines to rapidly access new chemical space for drug discovery efforts. Chem Commun (Camb) 2018; 54:12954-12957. [PMID: 30375586 DOI: 10.1039/c8cc07063f] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Multicomponent reactions (MCRs) are robust tools for the rapid synthesis of complex, small molecule libraries for use in drug discovery and development. By utilizing MCR chemistry, we developed a protocol to functionalize the C-3 position of imidazo[1,2-a]pyridine through a three component, decarboxylation reaction involving imidazo[1,2-a]pyridine, glyoxalic acid, and boronic acid.
Collapse
Affiliation(s)
- Naresh Gunaganti
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA.
| | | | | | | | | | | | | |
Collapse
|
21
|
Yan W, Lakkaniga NR, Carlomagno F, Santoro M, McDonald NQ, Lv F, Gunaganti N, Frett B, Li HY. Insights into Current Tropomyosin Receptor Kinase (TRK) Inhibitors: Development and Clinical Application. J Med Chem 2018; 62:1731-1760. [PMID: 30188734 DOI: 10.1021/acs.jmedchem.8b01092] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The use of kinase-directed precision medicine has been heavily pursued since the discovery and development of imatinib. Annually, it is estimated that around ∼20 000 new cases of tropomyosin receptor kinase (TRK) cancers are diagnosed, with the majority of cases exhibiting a TRK genomic rearrangement. In this Perspective, we discuss current development and clinical applications for TRK precision medicine by providing the following: (1) the biological background and significance of the TRK kinase family, (2) a compilation of known TRK inhibitors and analysis of their cocrystal structures, (3) an overview of TRK clinical trials, and (4) future perspectives for drug discovery and development of TRK inhibitors.
Collapse
Affiliation(s)
- Wei Yan
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Francesca Carlomagno
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università Federico II , Via S Pansini 5 , 80131 Naples , Italy.,Istituto di Endocrinologia e Oncologia Sperimentale del CNR , Via S Pansini 5 , 80131 Naples , Italy
| | - Massimo Santoro
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università Federico II , Via S Pansini 5 , 80131 Naples , Italy
| | - Neil Q McDonald
- Signaling and Structural Biology Laboratory , The Francis Crick Institute , London NW1 1AT , U.K.,Institute of Structural and Molecular Biology, Department of Biological Sciences , Birkbeck College , Malet Street , London WC1E 7HX , U.K
| | - Fengping Lv
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Naresh Gunaganti
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , Arkansas 72205 , United States
| |
Collapse
|
22
|
Bharate JB, McConnell N, Naresh G, Zhang L, Lakkaniga NR, Ding L, Shah NP, Frett B, Li HY. Rational Design, Synthesis and Biological Evaluation of Pyrimidine-4,6-diamine derivatives as Type-II inhibitors of FLT3 Selective Against c-KIT. Sci Rep 2018; 8:3722. [PMID: 29487300 PMCID: PMC5829162 DOI: 10.1038/s41598-018-21839-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/12/2018] [Indexed: 12/19/2022] Open
Abstract
FMS-like Tyrosine Kinase 3 (FLT3) is a clinically validated target for acute myeloid leukemia (AML). Inhibitors targeting FLT3 have been evaluated in clinical studies and have exhibited potential to treat FLT3-driven AML. A frequent, clinical limitation is FLT3 selectivity, as concomitant inhibition of FLT3 and c-KIT is thought to cause dose-limiting myelosuppression. Through a rational design approach, novel FLT3 inhibitors were synthesized employing a pyridine/pyrimidine warhead. The most potent compound identified from the studies is compound 13a, which exhibited an IC50 value of 13.9 ± 6.5 nM against the FLT3 kinase with high selectivity over c-KIT. Mechanism of action studies suggested that 13a is a Type-II kinase inhibitor, which was also supported through computer aided drug discovery (CADD) efforts. Cell-based assays identified that 13a was potent on a variety of FLT3-driven cell lines with clinical relevance. We report herein the discovery and therapeutic evaluation of 4,6-diamino pyrimidine-based Type-II FLT3 inhibitors, which can serve as a FLT3-selective scaffold for further clinical development.
Collapse
Affiliation(s)
- Jaideep B Bharate
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA
| | - Nicholas McConnell
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA.,Department of Pharmacology and Toxicology, The University of Arizona, Tucson, AZ, 85721, USA
| | - Gunaganti Naresh
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA
| | - Lingtian Zhang
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA
| | - Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA
| | - Lucky Ding
- Division of Hematology/Oncology, University of California, San Francisco, CA, 94143, USA
| | - Neil P Shah
- Division of Hematology/Oncology, University of California, San Francisco, CA, 94143, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94115, USA
| | - Brendan Frett
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA.
| |
Collapse
|