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Bijak V, Szczygiel M, Lenkiewicz J, Gucwa M, Cooper DR, Murzyn K, Minor W. The current role and evolution of X-ray crystallography in drug discovery and development. Expert Opin Drug Discov 2023; 18:1221-1230. [PMID: 37592849 PMCID: PMC10620067 DOI: 10.1080/17460441.2023.2246881] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
INTRODUCTION Macromolecular X-ray crystallography and cryo-EM are currently the primary techniques used to determine the three-dimensional structures of proteins, nucleic acids, and viruses. Structural information has been critical to drug discovery and structural bioinformatics. The integration of artificial intelligence (AI) into X-ray crystallography has shown great promise in automating and accelerating the analysis of complex structural data, further improving the efficiency and accuracy of structure determination. AREAS COVERED This review explores the relationship between X-ray crystallography and other modern structural determination methods. It examines the integration of data acquired from diverse biochemical and biophysical techniques with those derived from structural biology. Additionally, the paper offers insights into the influence of AI on X-ray crystallography, emphasizing how integrating AI with experimental approaches can revolutionize our comprehension of biological processes and interactions. EXPERT OPINION Investing in science is crucially emphasized due to its significant role in drug discovery and advancements in healthcare. X-ray crystallography remains an essential source of structural biology data for drug discovery. Recent advances in biochemical, spectroscopic, and bioinformatic methods, along with the integration of AI techniques, hold the potential to revolutionize drug discovery when effectively combined with robust data management practices.
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Affiliation(s)
- Vanessa Bijak
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Michal Szczygiel
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
| | - Joanna Lenkiewicz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Michal Gucwa
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
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Liu R, Sun X, Hu Z, Peng C, Wu T. Knockdown of long non-coding RNA MIR155HG suppresses melanoma cell proliferation, and deregulated MIR155HG in melanoma is associated with M1/M2 balance and macrophage infiltration. Cells Dev 2022; 170:203768. [DOI: 10.1016/j.cdev.2022.203768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/25/2021] [Accepted: 02/14/2022] [Indexed: 12/24/2022]
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Bhatia S, Pavlick AC, Boasberg P, Thompson JA, Mulligan G, Pickard MD, Faessel H, Dezube BJ, Hamid O. A phase I study of the investigational NEDD8-activating enzyme inhibitor pevonedistat (TAK-924/MLN4924) in patients with metastatic melanoma. Invest New Drugs 2016; 34:439-49. [PMID: 27056178 PMCID: PMC4919369 DOI: 10.1007/s10637-016-0348-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/18/2016] [Indexed: 12/31/2022]
Abstract
Purpose The therapeutic index of proteasome inhibitors may be improved through selective inhibition of a sub-component of the ubiquitin-proteasome system, such as the NEDD8-conjugation pathway. This multicenter, phase I, dose-escalation study assessed safety and the maximum tolerated dose (MTD), pharmacokinetics, pharmacodynamics, and antitumor activity of pevonedistat, an investigational NEDD8-activating enzyme (NAE) inhibitor, in patients with metastatic melanoma. Methods Patients received intravenous pevonedistat on Days 1, 4, 8, 11 (schedule A) or 1, 8, 15 (schedule B) of 21-day cycles. Results 26 patients received pevonedistat 50–278 mg/m2 on schedule A; 11 patients received pevonedistat 157 mg/m2 on schedule B. The schedule A MTD was 209 mg/m2: dose-limiting toxicities (DLTs) included grade 3 hypophosphatemia and grade 3 increased blood creatinine (associated with grade 3 hyperbilirubinemia). Two schedule A patients experienced acute organ failure toxicities, one of whom experienced grade 5 acute renal failure. Dose escalation did not occur in schedule B: DLTs included grade 3 myocarditis, grade 2 acute renal failure, and grade 2 hyperbilirubinemia in a single patient. Pevonedistat pharmacokinetics were approximately dose-proportional across the dose range studied, with a biphasic disposition profile characterized by a short elimination half-life (~10 h). Pharmacodynamic studies showed increases in NAE-regulated transcripts post-treatment; all post-dose biopsy samples were positive for pevonedistat-NEDD8 adduct. One schedule A patient achieved a partial response; 15 patients had stable disease (4 lasting ≥6.5 months). Conclusions Pevonedistat was generally well tolerated at the MTD. Anticipated pharmacodynamic effects of NAE inhibition were observed with single-agent pevonedistat in peripheral blood and tumor tissue.
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Affiliation(s)
- Shailender Bhatia
- Department of Medicine/Medical Oncology, University of Washington Medical Center/Fred Hutchinson Cancer Research Center/Seattle Cancer Care Alliance, 825 Eastlake Ave W, G4-830, Seattle, WA, 98109-1023, USA.
| | - Anna C Pavlick
- Departments of Medicine (Perlmutter Cancer Center) and Dermatology, NYU Langone Medical Center, New York, NY, USA
| | - Peter Boasberg
- The Angeles Clinic and Research Institute, Translational Research & Cutaneous Oncology, Los Angeles, CA, USA
| | - John A Thompson
- Department of Medicine/Medical Oncology, University of Washington Medical Center/Fred Hutchinson Cancer Research Center/Seattle Cancer Care Alliance, 825 Eastlake Ave W, G4-830, Seattle, WA, 98109-1023, USA
| | - George Mulligan
- Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, USA
| | - Michael D Pickard
- Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, USA
| | - Hélène Faessel
- Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, USA
| | - Bruce J Dezube
- Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, USA
| | - Omid Hamid
- The Angeles Clinic and Research Institute, Translational Research & Cutaneous Oncology, Los Angeles, CA, USA
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The outcomes of Polish patients with advanced BRAF-positive melanoma treated with vemurafenib in a safety clinical trial. Contemp Oncol (Pozn) 2015; 19:280-3. [PMID: 26557775 PMCID: PMC4631301 DOI: 10.5114/wo.2015.54082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 04/05/2015] [Accepted: 07/20/2015] [Indexed: 11/17/2022] Open
Abstract
AIM OF THE STUDY The BRAF inhibitor vemurafenib has improved progression-free survival and overall survival in patients with BRAFV600-mutation-positive metastatic melanoma. Here we present the results of an open-label safety study with vemurafenib in patients with metastatic melanoma enrolled in Polish oncological centres. MATERIAL AND METHODS Patients with untreated or previously treated Stage IIIC/IV BRAFV600 mutation-positive melanoma were treated with oral vemurafenib in an initial dose of 960 mg twice daily. Assessments for safety and efficacy were made every 28 days. For the survival analysis the Kaplan-Meier estimator was used with the log-rank tests for bivariate comparisons. RESULTS In total, 75 Polish patients were enrolled in the safety study across four centres. At data cut-off, 28 patients died (37%), mainly (26) due to disease progression; 33 (44%) patients continued vemurafenib after disease progression. The objective response rate was 46%, including two patients with a complete response and 29 with a partial response. Median progression-free survival was 7.4 months. The one-year overall survival rate was 61.9% (median overall survival was not reached). Seventy-three (97.3%) patients reported adverse events (AEs), and grade 3-5 toxicity was reported in 49.4% (37) patients. The most common AEs were: skin lesions (including rash and photosensitivity), arthralgia, and fatigue. CONCLUSIONS The overall safety profile and response rate of vemurafenib were comparable to those reported in previous studies of this drug. Our study confirmed the value of well-established prognostic features for overall survival, such as initial LDH (lactate dehydrogenase) level and AJCC staging.
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Tabolacci C, Cordella M, Turcano L, Rossi S, Lentini A, Mariotti S, Nisini R, Sette G, Eramo A, Piredda L, De Maria R, Facchiano F, Beninati S. Aloe-emodin exerts a potent anticancer and immunomodulatory activity on BRAF-mutated human melanoma cells. Eur J Pharmacol 2015; 762:283-92. [PMID: 26048310 DOI: 10.1016/j.ejphar.2015.05.057] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 12/18/2022]
Abstract
Aim of this study was to extend the knowledge on the antineoplastic effect of aloe-emodin (AE), a natural hydroxyanthraquinone compound, both in metastatic human melanoma cell lines and in primary stem-like cells (melanospheres). Treatment with AE caused reduction of cell proliferation and induction of SK-MEL-28 and A375 cells differentiation, characterized by a marked increase of transamidating activity of transglutaminase whose expression remained unmodified. In vitro antimetastatic property of AE was evaluated by adhesion and Boyden chamber invasion assays. The effect of AE on melanoma cytokines/chemokines production was determined by a multiplex assay: interestingly AE showed an immunomodulatory activity through GM-CSF and IFN-γ production. We report also that AE significantly reduced the proliferation, stemness and invasive potential of melanospheres. Moreover, AE treatment significantly enhanced dabrafenib (a BRAF inhibitor) antiproliferative activity in BRAF mutant cell lines. Our results confirm that AE possesses remarkable antineoplastic properties against melanoma cells, indicating this anthraquinone as a promising agent for differentiation therapy of cancer, or as adjuvant in chemotherapy and targeted therapy. Further, its mechanisms of action support a potential efficacy of AE treatment to counteract resistance of BRAF-mutated melanoma cells to target therapy.
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Affiliation(s)
- Claudio Tabolacci
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy; Department of Biology, University "Tor Vergata", Rome, Italy
| | - Martina Cordella
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Lorenzo Turcano
- Department of Biology, University "Tor Vergata", Rome, Italy
| | - Stefania Rossi
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Sabrina Mariotti
- Department of Infectious, Parasitic, and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Roberto Nisini
- Department of Infectious, Parasitic, and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Adriana Eramo
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Lucia Piredda
- Department of Biology, University "Tor Vergata", Rome, Italy
| | | | - Francesco Facchiano
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy.
| | - Simone Beninati
- Department of Biology, University "Tor Vergata", Rome, Italy
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Malemud CJ, Blumenthal DE. Protein kinase small molecule inhibitors for rheumatoid arthritis: Medicinal chemistry/clinical perspectives. World J Orthop 2014; 5:496-503. [PMID: 25232525 PMCID: PMC4133455 DOI: 10.5312/wjo.v5.i4.496] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 02/28/2014] [Accepted: 06/20/2014] [Indexed: 02/06/2023] Open
Abstract
Medicinal chemistry strategies have contributed to the development, experimental study of and clinical trials assessment of the first type of protein kinase small molecule inhibitor to target the Janus kinase/Signal Transducers and Activators of Transcription (JAK/STAT) signaling pathway. The orally administered small molecule inhibitor, tofacitinib, is the first drug to target the JAK/STAT pathway for entry into the armamentarium of the medical therapy of rheumatoid arthritis. The introduction of tofacitinib into general rheumatologic practice coupled with increasing understanding that additional cellular signal transduction pathways including the mitogen-activated protein kinase and phosphatidylinositide-3-kinase/Akt/mammalian target of rapamycin pathways as well as spleen tyrosine kinase also contribute to immune-mediated inflammatory in rheumatoid arthritis makes it likely that further development of orally administered protein kinase small molecule inhibitors for rheumatoid arthritis will occur in the near future.
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Rutkowski P, Blank C. Dabrafenib for the treatment of BRAF V600-positive melanoma: a safety evaluation. Expert Opin Drug Saf 2014; 13:1249-58. [PMID: 25014231 DOI: 10.1517/14740338.2014.939954] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION V-raf murine sarcoma viral oncogene homolog B1 (BRAF) inhibitors are emerging as the standard of care for treating advanced melanomas harboring the BRAF V600 oncogenic mutation. Dabrafenib is the second approved selective BRAF inhibitor (after vemurafenib) for the treatment of unresectable or metastatic BRAF V600-positive melanoma. AREAS COVERED This review covers the current data on the efficacy and safety of the selective BRAF inhibitor dabrafenib in patients with metastatic BRAF V600 positive melanoma. The pharmacological, safety and efficacy data are discussed from Phase I, II, and III studies of dabrafenib monotherapy as well as in combination with the MEK inhibitor trametinib. EXPERT OPINION Dabrafenib has demonstrated comparable efficacy to vemurafenib in BRAF V600E mutant melanoma patients. Dabrafenib is well tolerated in patients with metastatic melanoma, including patients with brain metastases. Nevertheless side effects are common, but usually manageable. In the Phase III study testing dabrafenib, 53% of patients reported grade 2 or higher adverse events (AEs). Toxicities were similar to those seen in the early-phase trials, with the most common being cutaneous manifestations (hyperkeratosis, papillomas, palmar-plantar erythrodysesthesia), pyrexia, fatigue, headache, and arthralgia. Combining a BRAF inhibitor with a MEK inhibitor, which may block paradoxical MAPK activation in BRAF wild type (skin) cells, may lower the incidence of squamoproliferative eruptions.
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Affiliation(s)
- Piotr Rutkowski
- Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Department of Soft Tissue/Bone Sarcoma and Melanoma , Roentgena 5, 02-781 Warsaw , Poland +48 22 6439375 ; +48 22 6439791 ;
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Etnyre D, Stone AL, Fong JT, Jacobs RJ, Uppada SB, Botting GM, Rajanna S, Moravec DN, Shambannagari MR, Crees Z, Girard J, Bertram C, Puri N. Targeting c-Met in melanoma: mechanism of resistance and efficacy of novel combinatorial inhibitor therapy. Cancer Biol Ther 2014; 15:1129-41. [PMID: 24914950 PMCID: PMC4128856 DOI: 10.4161/cbt.29451] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Numerous tyrosine kinase inhibitors (TKIs) targeting c-Met are currently in clinical trials for several cancers. Their efficacy is limited due to the development of resistance. The present study aims to elucidate this mechanism of c-Met TKI resistance by investigating key mTOR and Wnt signaling proteins in melanoma cell lines resistant to SU11274, a c-Met TKI. Xenografts from RU melanoma cells treated with c-Met TKIs SU11274 and JNJ38877605 showed a 7- and 6-fold reduction in tumor size, respectively. Resistant cells displayed upregulation of phosphorylated c-Met, mTOR, p70S6Kinase, 4E-BP1, ERK, LRP6, and active β-catenin. In addition, GATA-6, a Wnt signaling regulator, was upregulated, and Axin, a negative regulator of the Wnt pathway, was downregulated in resistant cells. Modulation of these mTOR and Wnt pathway proteins was also prevented by combination treatment with SU11274, everolimus, an mTOR inhibitor, and XAV939, a Wnt inhibitor. Treatment with everolimus, resulted in 56% growth inhibition, and a triple combination of SU11274, everolimus and XAV939, resulted in 95% growth inhibition in RU cells. The V600E BRAF mutation was found to be positive only in MU cells. Combination treatment with a c-Met TKI and a BRAF inhibitor displayed a synergistic effect in reducing MU cell viability. These studies indicate activation of mTOR and Wnt signaling pathways in c-Met TKI resistant melanoma cells and suggest that concurrent targeting of c-Met, mTOR, and Wnt pathways and BRAF may improve efficacy over traditional TKI monotherapy in melanoma patients.
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Affiliation(s)
- Deven Etnyre
- Department of Biomedical Sciences; University of Illinois College of Medicine; Rockford, IL USA
| | - Amanda L Stone
- Department of Biomedical Sciences; University of Illinois College of Medicine; Rockford, IL USA
| | - Jason T Fong
- Department of Biomedical Sciences; University of Illinois College of Medicine; Rockford, IL USA
| | - Ryan J Jacobs
- Department of Biomedical Sciences; University of Illinois College of Medicine; Rockford, IL USA
| | - Srijayaprakash B Uppada
- Department of Biomedical Sciences; University of Illinois College of Medicine; Rockford, IL USA
| | - Gregory M Botting
- Department of Biomedical Sciences; University of Illinois College of Medicine; Rockford, IL USA
| | - Supriya Rajanna
- Department of Biomedical Sciences; University of Illinois College of Medicine; Rockford, IL USA
| | - David N Moravec
- Department of Biomedical Sciences; University of Illinois College of Medicine; Rockford, IL USA
| | - Manohar R Shambannagari
- Department of Biomedical Sciences; University of Illinois College of Medicine; Rockford, IL USA
| | - Zachary Crees
- Department of Biomedical Sciences; University of Illinois College of Medicine; Rockford, IL USA
| | - Jennifer Girard
- Department of Biomedical Sciences; University of Illinois College of Medicine; Rockford, IL USA
| | - Ceyda Bertram
- Department of Biomedical Sciences; University of Illinois College of Medicine; Rockford, IL USA
| | - Neelu Puri
- Department of Biomedical Sciences; University of Illinois College of Medicine; Rockford, IL USA
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Wolchok JD, Hodi FS, Weber JS, Allison JP, Urba WJ, Robert C, O'Day SJ, Hoos A, Humphrey R, Berman DM, Lonberg N, Korman AJ. Development of ipilimumab: a novel immunotherapeutic approach for the treatment of advanced melanoma. Ann N Y Acad Sci 2013; 1291:1-13. [PMID: 23772560 PMCID: PMC3910157 DOI: 10.1111/nyas.12180] [Citation(s) in RCA: 220] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The immunotherapeutic agent ipilimumab has helped address a significant unmet need in the treatment of advanced melanoma. Ipilimumab is a fully human monoclonal antibody that targets cytotoxic T-lymphocyte antigen-4 (CTLA-4), thereby augmenting antitumor immune responses. After decades in which a number of clinical trials were conducted, ipilimumab was the first therapy to improve overall survival in a randomized, controlled phase III trial of patients with advanced melanoma. These results led to the regulatory approval of ipilimumab at 3 mg/kg for the treatment of unresectable or metastatic melanoma. More than 17,000 patients worldwide have received ipilimumab, either as a commercial drug at 3 mg/kg or in clinical trials and expanded access programs at different doses. Consistent with its proposed mechanism of action, the most common toxicities associated with ipilimumab therapy are inflammatory in nature. These immune-related adverse events were mostly reversible when effective treatment guidelines were followed. Importantly, long-term follow-up of patients who received ipilimumab in a phase III trial showed that 24% survived at least two years, and in phase II studies, a proportion of patients survived at least five years. Evaluation of ipilimumab is ongoing in the adjuvant setting for melanoma, and for advanced disease in nonsmall cell lung, small cell lung, prostate, ovarian, and gastric cancers.
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Affiliation(s)
- Jedd D Wolchok
- Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.
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