1
|
Rasul HO, Ghafour DD, Aziz BK, Hassan BA, Rashid TA, Kivrak A. Decoding Drug Discovery: Exploring A-to-Z In Silico Methods for Beginners. Appl Biochem Biotechnol 2025; 197:1453-1503. [PMID: 39630336 DOI: 10.1007/s12010-024-05110-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2024] [Indexed: 03/29/2025]
Abstract
The drug development process is a critical challenge in the pharmaceutical industry due to its time-consuming nature and the need to discover new drug potentials to address various ailments. The initial step in drug development, drug target identification, often consumes considerable time. While valid, traditional methods such as in vivo and in vitro approaches are limited in their ability to analyze vast amounts of data efficiently, leading to wasteful outcomes. To expedite and streamline drug development, an increasing reliance on computer-aided drug design (CADD) approaches has merged. These sophisticated in silico methods offer a promising avenue for efficiently identifying viable drug candidates, thus providing pharmaceutical firms with significant opportunities to uncover new prospective drug targets. The main goal of this work is to review in silico methods used in the drug development process with a focus on identifying therapeutic targets linked to specific diseases at the genetic or protein level. This article thoroughly discusses A-to-Z in silico techniques, which are essential for identifying the targets of bioactive compounds and their potential therapeutic effects. This review intends to improve drug discovery processes by illuminating the state of these cutting-edge approaches, thereby maximizing the effectiveness and duration of clinical trials for novel drug target investigation.
Collapse
Affiliation(s)
- Hezha O Rasul
- Department of Pharmaceutical Chemistry, College of Science, Charmo University, Peshawa Street, Chamchamal, 46023, Sulaimani, Iraq.
| | - Dlzar D Ghafour
- Department of Medical Laboratory Science, College of Science, Komar University of Science and Technology, 46001, Sulaimani, Iraq
- Department of Chemistry, College of Science, University of Sulaimani, 46001, Sulaimani, Iraq
| | - Bakhtyar K Aziz
- Department of Nanoscience and Applied Chemistry, College of Science, Charmo University, Peshawa Street, Chamchamal, 46023, Sulaimani, Iraq
| | - Bryar A Hassan
- Computer Science and Engineering Department, School of Science and Engineering, University of Kurdistan Hewler, KRI, Iraq
- Department of Computer Science, College of Science, Charmo University, Peshawa Street, Chamchamal, 46023, Sulaimani, Iraq
| | - Tarik A Rashid
- Computer Science and Engineering Department, School of Science and Engineering, University of Kurdistan Hewler, KRI, Iraq
| | - Arif Kivrak
- Department of Chemistry, Faculty of Sciences and Arts, Eskisehir Osmangazi University, Eskişehir, 26040, Turkey
| |
Collapse
|
2
|
Mohamed MA, Elsaman T, Elderdery AY, Alsrhani A, Ghanem HB, Alruwaili MM, Hamza SMA, Mekki SEI, Alotaibi HA, Mills J. Unveiling the Anticancer Potential: Computational Exploration of Nitrogenated Derivatives of (+)-Pancratistatin as Topoisomerase I Inhibitors. Int J Mol Sci 2024; 25:10779. [PMID: 39409108 PMCID: PMC11476810 DOI: 10.3390/ijms251910779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2024] [Revised: 10/03/2024] [Accepted: 10/05/2024] [Indexed: 10/20/2024] Open
Abstract
Cancer poses a substantial global health challenge, driving the need for innovative therapeutic solutions that offer improved effectiveness and fewer side effects. Topoisomerase I (Topo I) has emerged as a validated molecular target in the pursuit of developing anticancer drugs due to its critical role in DNA replication and transcription. (+)-Pancratistatin (PST), a naturally occurring compound found in various Amaryllidaceae plants, exhibits promising anticancer properties by inhibiting Topo I activity. However, its clinical utility is hindered by issues related to limited chemical availability and aqueous solubility. To address these challenges, molecular modelling techniques, including virtual screening, molecular docking, molecular mechanics with generalised born and surface area solvation (MM-GBSA) calculations, and molecular dynamics simulations were utilised to evaluate the binding interactions and energetics of PST analogues with Topo I, comparing them with the well-known Topo I inhibitor, Camptothecin. Among the compounds screened for this study, nitrogenated analogues emerged as the most encouraging drug candidates, exhibiting improved binding affinities, favourable interactions with the active site of Topo I, and stability of the protein-ligand complex. Structural analysis pinpointed key molecular determinants responsible for the heightened potency of nitrogenated analogues, shedding light on essential structural modifications for increased activity. Moreover, in silico absorption, distribution, metabolism, excretion, and toxicity (ADMET) predictions highlighted favourable drug-like properties and reduced toxicity profiles for the most prominent nitrogenated analogues, further supporting their potential as effective anticancer agents. In summary, this screening study underscores the significance of nitrogenation in augmenting the anticancer efficacy of PST analogues targeting Topo I. The identified lead compounds exhibit significant potential for subsequent experimental validation and optimisation, thus facilitating the development of novel and efficacious anticancer therapeutics with enhanced pharmacological profiles.
Collapse
Affiliation(s)
- Magdi Awadalla Mohamed
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka 72388, Saudi Arabia
| | - Tilal Elsaman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka 72388, Saudi Arabia
| | - Abozer Y. Elderdery
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 42421, Saudi Arabia; (A.Y.E.); (A.A.); (H.B.G.)
| | - Abdullah Alsrhani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 42421, Saudi Arabia; (A.Y.E.); (A.A.); (H.B.G.)
| | - Heba Bassiony Ghanem
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 42421, Saudi Arabia; (A.Y.E.); (A.A.); (H.B.G.)
| | - Majed Mowanes Alruwaili
- Nursing Administration & Education Department, College of Nursing, Jouf University, Sakaka 72388, Saudi Arabia;
| | - Siddiqa M. A. Hamza
- Department of Pathology, College of Medicine, Umm Alqura University, Algunfudah 21912, Saudi Arabia;
| | | | | | - Jeremy Mills
- School of Medicine, Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK;
| |
Collapse
|
3
|
Doan NQH, Tran HN, Nguyen NTM, Pham TM, Nguyen QDK, Vu TT. Synthesis, Antimicrobial - Cytotoxic Evaluation, and Molecular Docking Studies of Quinolin-2-one Hydrazones Containing Nitrophenyl or Isonicotinoyl/Nicotinoyl Moiety. Chem Biodivers 2024; 21:e202401142. [PMID: 39032128 DOI: 10.1002/cbdv.202401142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 07/12/2024] [Accepted: 07/19/2024] [Indexed: 07/22/2024]
Abstract
By applying the hybrid molecular strategy, in this study, we reported the synthesis of fifteen quinolin-2-one hydrazones containing nitrophenyl or nicotinonyl/isonicotinoyl moiety, followed by in vitro and in silico evaluations of their potential antimicrobial and anticancer activities. In vitro antimicrobial evaluation of the target compounds on seven pathogenic strains, applying the broth microdilution method, revealed that compound 4a demonstrated the most potential antifungal activity against C. albicans (MIC 512 μg mL-1) and C. krusei (MIC 128 μg mL-1). In vitro cytotoxic evaluation of the target compounds on three human cancer cell lines, employing the MTT method, suggested that compound 5c exhibited the most potential cytotoxicities against HepG2 (IC50 10.19 μM), A549 (IC50 20.43 μM), and MDA-MB-231 (IC50 16.82 μM) cells. Additionally, molecular docking studies were performed to investigate the binding characteristics of compounds 4a and 5c with fungal lanosterol 14α-demethylase and human topoisomerase I-II, respectively, thereby contributing to the elucidation of their in vitro antifungal and cytotoxic properties. Furthermore, compounds 4a and 5c, via SwissADME prediction, could exhibit favorable physicochemical and pharmacokinetic properties. In conclusion, this study provides valuable insights into the potential of quinolin-2-one hydrazones as promising candidates for the development of novel antimicrobial and anticancer agents in the future.
Collapse
Affiliation(s)
- Nam Q H Doan
- Faculty of Pharmacy, Van Lang University, 69/68 Dang Thuy Tram Street, Ward 13, Binh Thanh District, Ho Chi Minh City, 70000, Vietnam
| | - Hoan N Tran
- Faculty of Pharmacy, Van Lang University, 69/68 Dang Thuy Tram Street, Ward 13, Binh Thanh District, Ho Chi Minh City, 70000, Vietnam
| | - Nhu T M Nguyen
- Faculty of Pharmacy, Van Lang University, 69/68 Dang Thuy Tram Street, Ward 13, Binh Thanh District, Ho Chi Minh City, 70000, Vietnam
| | - Thu M Pham
- Faculty of Pharmacy, Van Lang University, 69/68 Dang Thuy Tram Street, Ward 13, Binh Thanh District, Ho Chi Minh City, 70000, Vietnam
| | - Quyen D K Nguyen
- Faculty of Pharmacy, Van Lang University, 69/68 Dang Thuy Tram Street, Ward 13, Binh Thanh District, Ho Chi Minh City, 70000, Vietnam
| | - Thanh-Thao Vu
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, 41-43 Dinh Tien Hoang Street, Ben Nghe Ward, District 1, Ho Chi Minh City, 70000, Vietnam
| |
Collapse
|
4
|
Bali SK, Martin R, Almeida NMS, Saunders C, Wilson AK. Per- and Polyfluoroalkyl (PFAS) Disruption of Thyroid Hormone Synthesis. ACS OMEGA 2024; 9:39554-39563. [PMID: 39346893 PMCID: PMC11425649 DOI: 10.1021/acsomega.4c03578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 08/03/2024] [Accepted: 08/08/2024] [Indexed: 10/01/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are a group of environmental pollutants that have been linked to a variety of health problems in humans, including the disruption of thyroid functions. Herein, for the first time, the impact of PFAS on thyroid hormone synthesis is shown. Mid- to long-chain PFAS impact thyroid hormone synthesis by changing the local hydrogen bond network as well as the required orientation of hormonogenic residues, stopping the production of thyroxine (T4). Furthermore, the toxic effects of sulfonic PFAS are more prominent than those of carboxylic PFAS, highlighting that the exposure to these specific compounds can pose greater problems for thyroid homeostasis.
Collapse
Affiliation(s)
- Semiha Kevser Bali
- Department of Chemistry and MSU Center for PFAS Research, Michigan State University, East Lansing, Michigan 48864, United States
| | - Rebecca Martin
- Department of Chemistry and MSU Center for PFAS Research, Michigan State University, East Lansing, Michigan 48864, United States
| | - Nuno M S Almeida
- Department of Chemistry and MSU Center for PFAS Research, Michigan State University, East Lansing, Michigan 48864, United States
| | - Catherine Saunders
- Department of Chemistry and MSU Center for PFAS Research, Michigan State University, East Lansing, Michigan 48864, United States
| | - Angela K Wilson
- Department of Chemistry and MSU Center for PFAS Research, Michigan State University, East Lansing, Michigan 48864, United States
| |
Collapse
|
5
|
Bali S, Hall K, Massoud RI, Almeida NMS, Wilson AK. Interaction of Per- and Polyfluoroalkyl Substances with Estrogen Receptors in Rainbow Trout ( Oncorhynchus mykiss): An In Silico Investigation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:15960-15970. [PMID: 39207093 PMCID: PMC11394024 DOI: 10.1021/acs.est.4c03648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024]
Abstract
Fresh water sources, including lakes, such as the Great Lakes, are some of the most important ecosystems in the world. Despite the importance of these lakes, there is increasing concern about the presence of per- and polyfluoroalkyl substances (PFAS)─among the most prevalent contaminants of our time─due to the ability of PFAS to bioaccumulate and persist in the environment, as well as to its linkages to detrimental human and animal health effects. In this study, PFAS exposure on rainbow trout (Oncorhynchus mykiss) is examined at the molecular level, focusing on the impact of PFAS binding on the alpha (α) and beta (β) estrogen receptors (ERs) using molecular dynamics simulations, binding free energy calculations, and structural analysis. ERs are involved in fundamental physiological processes, including reproductive system development, muscle regeneration, and immunity. This study shows that PFAS binds to both the estrogen α and estrogen β receptors, albeit via different binding modes, due to a modification of an amino acid in the binding site as a result of a reorientation of residues in the binding pocket. As ER overactivation can occur through environmental toxins and pollutants, this study provides insights into the influence of different types of PFAS on protein function.
Collapse
Affiliation(s)
- Semiha
Kevser Bali
- Department of Chemistry, Michigan
State University, East Lansing, Michigan 48824, United States
| | - Kyleen Hall
- Department of Chemistry, Michigan
State University, East Lansing, Michigan 48824, United States
| | - Rana I. Massoud
- Department of Chemistry, Michigan
State University, East Lansing, Michigan 48824, United States
| | - Nuno M. S. Almeida
- Department of Chemistry, Michigan
State University, East Lansing, Michigan 48824, United States
| | - Angela K. Wilson
- Department of Chemistry, Michigan
State University, East Lansing, Michigan 48824, United States
| |
Collapse
|
6
|
Almeida NMS, Bali SK, James D, Wang C, Wilson AK. Binding of Per- and Polyfluoroalkyl Substances (PFAS) to the PPARγ/RXRα-DNA Complex. J Chem Inf Model 2023; 63:7423-7443. [PMID: 37990410 DOI: 10.1021/acs.jcim.3c01384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Nuclear receptors are the fundamental building blocks of gene expression regulation and the focus of many drug targets. While binding to DNA, nuclear receptors act as transcription factors, governing a multitude of functions in the human body. Peroxisome proliferator-activator receptor γ (PPARγ) and the retinoid X receptor α (RXRα) form heterodimers with unique properties and have a primordial role in insulin sensitization. This PPARγ/RXRα heterodimer has been shown to be impacted by per- and polyfluoroalkyl substances (PFAS) and linked to a variety of significant health conditions in humans. Herein, a selection of the most common PFAS (legacy and emerging) was studied utilizing molecular dynamics simulations for PPARγ/RXRα. The local and global structural effects of PFAS binding on the known ligand binding pockets of PPARγ and RXRα as well as the DNA binding domain (DBD) of RXRα were inspected. The binding free energies were predicted computationally and were compared between the different binding pockets. In addition, two electronic structure approaches were utilized to model the interaction of PFAS within the DNA binding domain, density functional theory (DFT) and domain-based pair natural orbital coupled cluster with perturbative triples (DLPNO-CCSD(T)) approaches, with implicit solvation. Residue decomposition and hydrogen-bonding analysis were also performed, detailing the role of prominent residues in molecular recognition. The role of l-carnitine is explored as a potential in vivo remediation strategy for PFAS interaction with the PPARγ/RXRα heterodimer. In this work, it was found that PFAS can bind and act as agonists for all of the investigated pockets. For the first time in the literature, PFAS are postulated to bind to the DNA binding domain in a nonspecific manner. In addition, for the PPARγ ligand binding domain, l-carnitine shows promise in replacing smaller PFAS from the pocket.
Collapse
Affiliation(s)
- Nuno M S Almeida
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
| | - Semiha Kevser Bali
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
| | - Deepak James
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
| | - Cong Wang
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
| | - Angela K Wilson
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
| |
Collapse
|
7
|
Lee HM, Wright WC, Pan M, Low J, Currier D, Fang J, Singh S, Nance S, Delahunty I, Kim Y, Chapple RH, Zhang Y, Liu X, Steele JA, Qi J, Pruett-Miller SM, Easton J, Chen T, Yang J, Durbin AD, Geeleher P. A CRISPR-drug perturbational map for identifying compounds to combine with commonly used chemotherapeutics. Nat Commun 2023; 14:7332. [PMID: 37957169 PMCID: PMC10643606 DOI: 10.1038/s41467-023-43134-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Combination chemotherapy is crucial for successfully treating cancer. However, the enormous number of possible drug combinations means discovering safe and effective combinations remains a significant challenge. To improve this process, we conduct large-scale targeted CRISPR knockout screens in drug-treated cells, creating a genetic map of druggable genes that sensitize cells to commonly used chemotherapeutics. We prioritize neuroblastoma, the most common extracranial pediatric solid tumor, where ~50% of high-risk patients do not survive. Our screen examines all druggable gene knockouts in 18 cell lines (10 neuroblastoma, 8 others) treated with 8 widely used drugs, resulting in 94,320 unique combination-cell line perturbations, which is comparable to the largest existing drug combination screens. Using dense drug-drug rescreening, we find that the top CRISPR-nominated drug combinations are more synergistic than standard-of-care combinations, suggesting existing combinations could be improved. As proof of principle, we discover that inhibition of PRKDC, a component of the non-homologous end-joining pathway, sensitizes high-risk neuroblastoma cells to the standard-of-care drug doxorubicin in vitro and in vivo using patient-derived xenograft (PDX) models. Our findings provide a valuable resource and demonstrate the feasibility of using targeted CRISPR knockout to discover combinations with common chemotherapeutics, a methodology with application across all cancers.
Collapse
Affiliation(s)
- Hyeong-Min Lee
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - William C Wright
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Min Pan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jonathan Low
- Department of Chemical Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Duane Currier
- Department of Chemical Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jie Fang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shivendra Singh
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Stephanie Nance
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ian Delahunty
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yuna Kim
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Richard H Chapple
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yinwen Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Xueying Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jacob A Steele
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Adam D Durbin
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Paul Geeleher
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| |
Collapse
|
8
|
Nipate DS, Rangan K, Kumar A. Copper(II)-Catalyzed Synthesis of Pyrrolo[3,4- b]quinolinediones from o-Amino Carbonyl Compounds and Maleimides. Org Lett 2023. [PMID: 36809005 DOI: 10.1021/acs.orglett.3c00240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
A copper(II)-catalyzed cascade synthesis of 1H-pyrrolo[3,4-b]quinoline-1,3(2H)-diones has been achieved from readily available o-amino carbonyl compounds and maleimides. This one-pot cascade strategy involves a copper-catalyzed aza-Michael addition followed by condensation and oxidation to deliver the target molecules. The protocol features a broad substrate scope and excellent functional group tolerance and affords products in moderate to good (44-88%) yields.
Collapse
Affiliation(s)
- Dhananjay S Nipate
- Department of Chemistry, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan 333031, India
| | - Krishnan Rangan
- Department of Chemistry, Birla Institute of Technology and Science Pilani, Hyderabad, Telangana 500078, India
| | - Anil Kumar
- Department of Chemistry, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan 333031, India
| |
Collapse
|
9
|
Jiang W, Cai G, Hu P, Wang Y. Personalized medicine of non-gene-specific chemotherapies for non-small cell lung cancer. Acta Pharm Sin B 2021; 11:3406-3416. [PMID: 34900526 PMCID: PMC8642451 DOI: 10.1016/j.apsb.2021.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/28/2020] [Accepted: 12/01/2020] [Indexed: 12/15/2022] Open
Abstract
Non-small cell lung cancer is recognized as the deadliest cancer across the globe. In some areas, it is more common in women than even breast and cervical cancer. Its rise, vaulted by smoking habits and increasing air pollution, has garnered much attention and resource in the medical field. The first lung cancer treatments were developed more than half a century ago. Unfortunately, many of the earlier chemotherapies often did more harm than good, especially when they were used to treat genetically unsuitable patients. With the introduction of personalized medicine, physicians are increasingly aware of when, how, and in whom, to use certain anti-cancer agents. Drugs such as tyrosine kinase inhibitors, anaplastic lymphoma kinase inhibitors, and monoclonal antibodies possess limited utility because they target specific oncogenic mutations, but other drugs that target mechanisms universal to all cancers do not. In this review, we discuss many of these non-oncogene-targeting anti-cancer agents including DNA replication inhibitors (i.e., alkylating agents and topoisomerase inhibitors) and cytoskeletal function inhibitors to highlight their application in the setting of personalized medicine as well as their limitations and resistance factors.
Collapse
Affiliation(s)
| | - Guiqing Cai
- Quest Diagnostics, San Juan Capistrano, CA 92675, USA
| | - Peter Hu
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yue Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
10
|
Ali AAA, Lee YR, Wu AT, Yadav VK, Yu DS, Huang HS. Structure-based strategies for synthesis, lead optimization and biological evaluation of N-substituted anthra[1,2-c][1,2,5]thiadiazole-6,11-dione derivatives as potential multi-target anticancer agents. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2020.10.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
11
|
Ugur I, Chandrasekhar P. Proton relay network in P450cam formed upon docking of putidaredoxin. Proteins 2019; 88:558-572. [PMID: 31597203 DOI: 10.1002/prot.25835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/13/2019] [Accepted: 09/28/2019] [Indexed: 11/08/2022]
Abstract
Cytochromes P450 are versatile heme-based enzymes responsible for vital life processes. Of these, P450cam (substrate camphor) has been most studied. Despite this, precise mechanisms of the key O─O cleavage step remain partly elusive to date; effects observed in various enzyme mutants remain partly unexplained. We have carried out extended (to 1000 ns) MM-MD and follow-on quantum mechanics/molecular mechanics computations, both on the well-studied FeOO state and on Cpd(0) (compound 0). Our simulations include (all camphor-bound): (a) WT (wild type), FeOO state. (b) WT, Cpd(0). (c) Pdx (Putidaredoxin, redox partner of P450)-docked-WT, FeOO state. (d) Pdx-docked WT, Cpd(0). (e) Pdx-docked T252A mutant, Cpd(0). Among our key findings: (a) Effect of Pdx docking appears to go far beyond that indicated in prior studies: it leads to specific alterations in secondary structure that create the crucial proton relay network. (b) Specific proton relay networks we identify are: FeOO(H)⋯T252⋯nH 2 O⋯D251 in WT; FeOO(H)⋯nH 2 O⋯D251 in T252A mutant; both occur with Pdx docking. (c) Direct interaction of D251 with -FeOOH is, respectively, rare/frequent in WT/T252A mutant. (d) In WT, T252 is in the proton relay network. (e) Positioning of camphor appears significant: when camphor is part of H-bonding network, second protonation appears to be facilitated.
Collapse
Affiliation(s)
- Ilke Ugur
- Research Division, Ashwin-Ushas Corporation, Marlboro, New Jersey
| | | |
Collapse
|