Hiện trạng của lĩnh vực nghiên cứu và phát triển thuốc có sự trợ giúp của máy tính

Nội dung text: Hiện trạng của lĩnh vực nghiên cứu và phát triển thuốc có sự trợ giúp của máy tính

1. Phạm Thị Ly, Lê Quốc Chơn / Tạp chí Khoa học và Công nghệ Đại học Duy Tân 4(47) (2021) 37-44 37 4(47) (2021) 37-44 Hiện trạng của lĩnh vực nghiên cứu và phát triển thuốc có sự trợ giúp của máy tính The current status of computer-aided drug design Phạm Thị Lya, Lê Quốc Chơna,b* Pham Thi Lya, Le Quoc Chona,b* aKhoa Dược, Trường Đại học Duy Tân, Đà Nẵng, Việt Nam aFaculty of Pharmacy, Duy Tan University, Da Nang, 550000, Vietnam bViện Nghiên cứu và Phát triển Công nghệ Cao, Trường Đại học Duy Tân, Đà Nẵng, Việt Nam bInstitute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam (Ngày nhận bài: 16/4/2021, ngày phản biện xong: 11/5/2021, ngày chấp nhận đăng: 22/7/2021) Tóm tắt Nhiều căn bệnh nguy hiểm hiện nay chưa có thuốc chữa trị. Theo WHO, năm 2019 bệnh tim mạch gây 9 triệu người chết chiếm 16% tổng số người chết của năm, ngoài ra bệnh tiểu đường và Alzheimer cũng nằm trong số các bệnh gây nhiều cái chết nhất. Do đó, việc tìm kiếm và phát triển các thuốc chữa bệnh hiệu quả luôn là cần thiết. Tuy nhiên, quy trình nghiên cứu và phát triển thuốc hiện nay tốn rất nhiều chi phí và thời gian. Để một loại thuốc mới ra đến được thị trường phải mất hơn 12 năm nghiên cứu và phát triển, chi phí tài chính hơn một tỉ đô la Mỹ. Vì vậy, mô phỏng máy tính được ứng dụng vào để tiết giảm chi phí tài chính và thời gian. Bài báo này khái quát các nguyên lý hoạt động, những đóng góp của ứng dụng máy tính trong nghiên cứu và phát triển thuốc. Chúng tôi cũng thảo luận những thử thách cần vượt qua để việc ứng dụng máy tính trong nghiên cứu và phát triển thuốc hiệu quả hơn. Từ khóa: Nghiên cứu thuốc; phát triển thuốc; thiết kế thuốc trên máy tính; gán phân tử; tương tác thuốc với protein. Abstract There are many diseases desperately needed treatment. In 2019, WHO reported that cardiovascular disease caused 9 million deaths and accounted for 16% the total mortality. The report also indicated that diabetes and Alzheimer are among the most deathly diseases, and pharmacotherapy has been known to be among the most effective treatment methods to combat against diseases. Thus, demand for the new drug has been always high and urgent, unfortunately, traditional method for drug discovery and development is time-consuming, expensive and inefficient. It takes more than 12 years and costs up to billions of USD to bring a new drug to patients. These drawbacks have been compensated for by Computer-aided drug design (CADD). This review summarizes the core working principles, the contributions, challenges and trends of CADD including structure-based and ligand-based drug design together with relevant softwares and databases of protein as well as ligands. Keywords: Computer - aided drug design; Structure - based drug design; Ligand - based drug design; Molecular docking. * Corresponding Author: Le Quoc Chon; Faculty of Pharmacy, Duy Tan University, Da Nang, 550000, Vietnam, Institute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam Email: lequocchon@dtu.edu.com
2. 38 Phạm Thị Ly, Lê Quốc Chơn / Tạp chí Khoa học và Công nghệ Đại học Duy Tân 4(47) (2021) 37-44 1. Introduction throughput screening (HTS). CADD sometimes New medication is extremely necessary shows more effectiveness than HTS, for because of many unmet medical needs such as example Doman et al. compared hit lists from cancer, cardiovascular diseases and antibiotic molecular docking with HTS and reported that resistance. Finding drugs by following the the docking hits were more druglike than those traditional process is a lengthy, costly, difficult from HTS [3]. In traditional DDD process, a and inefficient process regardless of the lead compound might be obtained out of around advancement of biotechnology and analytical 80,000 compounds and then goes through lead sciences. This process consumes over 1 billion optimization to improve its bioactivities and dollars and takes more than 12 years to bring a reduce toxicity [4]. This long and expensive new drug to the patients [1]. Figure 1 shows the process can be optimized by using CADD, workflow of the traditional process in drug reducing number of compounds that must be discovery and development (DDD). synthesized and tested [5]. Two major approaches in CADD are structure-based and ligand-based. 2. Structure-based drug design Structure–based drug design (SBDD) relies on structures of biological target, which is normally a protein whose 3D structure can be determined by X-ray crystallography and Nuclear Magnetic Resonance spectroscopy. Target and ligand molecules in molecular Figure 1: Traditional process of drug discovery docking are considered as “lock - and - key”, and development [1] where the target is the “lock” and the ligand is To streamline that process, computer- aided the “key”. The ligand adapts the conformation to drug design (CADD) has been applied widely achieve the best fit with the target. This fitness is in pharma and biotech companies to reduce cost expressed as binding modes and binding affinity and time involved in traditional method and between the target and the ligand. The ligands nowadays CADD is an indispensable part of that show the highest interaction with the targets pharmaceutical industry [2]. are selected, evaluated and ranked by scoring CADD has been used to find hit and lead function. Figure 2 shows the simplified compounds, which is also the goal of high - workflow of SBDD process. Figure 2: Process of structure-based drug design [6] consists of (i) choosing target molecule, (ii) preparing the ligand library, (iii) docking the ligands into the target to model the interaction and finally (iv) identifying hit compounds.
3. Phạm Thị Ly, Lê Quốc Chơn / Tạp chí Khoa học và Công nghệ Đại học Duy Tân 4(47) (2021) 37-44 39 One fundamental concept in molecular of machine learning algorithms such as super docking is scoring functions that are used to vector machine, random forest, artificial neural rank ligand molecules based on the binding network, and deep learning. affinity of these molecules to the target. There 3. Ligand-based drug design are 4 types of scoring functions: physical based, empirical based, knowledge based and machine Ligand-based drug design (LBDD), on the learning. The first three are classified as other hand, relies on knowledge of certain classical scoring functions, using linear ligands that show biological activities with a regression model, whilst the latter incorporates drug target. Based on structures of these nonlinear regression machine learning methods ligands, a pharmacophore model is built. Then, [7]. The force - field based scoring function chemical databases are scanned against the identifies binding energy by total of bonded, pharmacophore to find molecules that have electrostatic and van der Waals interactions [6], similar structure to the pharmacophore. These while empirical and knowledge - based molecules will be experimentally tested to functions calculate binding energy by confirm their biological activities, then follow hydrogen-bonding, ionic and apolar further development phases in drug discovery interactions, as well as desolvation and entropic process. Figure 3 shows the steps in LBDD effects [8]. Machine learning employs a variety process. Figure 3: Outline of the process in LBDD The critical factor of LBDD is pharmacophore modeling. An ideal pharmacophore model represents all features that are necessary to ensure the optimal molecular interactions with a target [9]. Six pharmacophoric features used to build a pharmacophore are hydrogen bond donors, hydrogen bond acceptors, acidic centers, basic centers, hydrophobic regions and aromatic ring centroids (Figure 4) [10]. Some popular Figure 4: Example of an pharmacophore model [11] pharmacophore searching softwares are Pharmer, PharmMapper, PharmaGist and ZINCPharma.
4. 40 Phạm Thị Ly, Lê Quốc Chơn / Tạp chí Khoa học và Công nghệ Đại học Duy Tân 4(47) (2021) 37-44 4. Ligand and protein databases for CADD with 441,942,016 sequences, 373,907,456 CADD needs ligand and target databases to sequences and 305,529 proteomes, respectively. work. Ligand databases store molecular IntAct focuses on protein - protein interaction, features, drugs’ mechanism of action, drug containing 22,037 publications, 1,130,596 indications, clinical data and other essential interactions and 119,281 interactors. All these information of small molecules. There are databases are public accessed. numerous sizable chemical databases available 5. Contributions of CADD today. ZINC, for example, has the greatest CADD economizes DDD process. number of ligands, containing over 200 million Application of CADD can save 30% the total 3D leadlike molecules and more than 700 cost and time invested in developing a new million 2D structures. Chemspider, Pubchem, drug [13]. Research reports that CADD market and REAXYS also have a large number of is increasing, from $1,540.4 billion in 2018 to molecules: 88, 103 and 118 millions, $4,878.5 billion in 2026 [14]. Nowadays, respectively [12]. CADD has been extensively applied in almost Similarly, protein databases contain the every phase of DDD process such as detecting essential information of protein such as targets, validation, lead discovery, and physical, chemical and biological information, optimization and preclinical tests [15]-[17]. three-dimensional structures, fold assignments, Comparing to HTS, CADD can provide active site, function, and protein - protein knowledge about molecular interaction between interaction. Some important databases are proteins and ligands, therefore interaction Protein Data Bank (PDB), RefSeq, UniProt, merchanism [18]. and IntAct. Nowadays, PDB contains about Searching for treatment of covid-19 in 2020, 173,537 biological macromolecular structures for instance, has used CADD [19]. Ahmed et al. and includes four members such as Research used CADD to demonstrate the potential of a Collaboratory for Structural Bioinformatics remdesivir and its derivatives in treating Protein Data Bank (RCSB PDB), Biological SAR-CoV-2 infection [20]. De et al. succeeded Magnetic Resonance Data Bank (BMRB), in using CADD for development anti-cancer Protein Data Bank in Europe (PDBe) and drugs [21]. The contributions of CADD has Protein Data Bank Japan (PDBj). RefSeq been demonstrated by the large amount of provides a comprehensive, integrated, non - medicines tested with supports of CADD. Table redundant, well - annotated set of sequences, 1 shows some medicines that are developed including 191,411,721 proteins, 35,353,412 with the support from CADD. transcripts and 106,581 organisms. UniProt is also a popular of sequence databases, Table 1: Successful medicines that have containing UniRef, UniParc and Proteomes support from CADD Medicine Biological action Approval Ref year Captopril An angiotensin-converting enzyme inhibitor, treat high 1981 [22] blood pressure. Dorolamide Inhibits carbonic anhydrase II and reduces intraocular 1994 [22] pressure. To treat ocular disease or glaucoma. Saquinavir Inhibits protease of rotavirus, that can inhibit one of the 1995 [22] last stages of viral replication.
5. Phạm Thị Ly, Lê Quốc Chơn / Tạp chí Khoa học và Công nghệ Đại học Duy Tân 4(47) (2021) 37-44 41 Zanamivir Inhibits neuraminidase enzyme of influenza virus, used for 1999 [22] treatment of influenza A or B viruses. Oseltamivir Has similar effect with zanamivir with an improvement of 1999 [22] bioavailability compared to zanamivir. [23] Aliskiren Use for treatment of hypertension by impacting on 2007 [22] renin-angiotensin system. [24] Boceprevir Boceprevir is antiviral medication used to treat chronic 2011 [22] Hepatitis C [25] Ritonavir Inhibits HIV protease and interferes the reproductive cycle 1996 [22] of HIV Tirofiban Tirofiban is an antiplatelet drug by inhibiting between 1998 [22] fibrinogen and platelet integrin receptor GP IIB/IIIa. Raltegravir An antiretroviral medication used together with other 2007 [22] medication, to treat HIV/AIDS. Loteprednol An ophthalmic corticosteroid formulation 2020 [26] etabonate Remdesivir A SARS-CoV-2 nucleotide analog RNA polymerase 2020 [20] inhibitor for the treatment of COVID-19 patients Fostesavir Treat HIV 2020 [27] Artesunate Treat severe malaria 2020 [28] Opicapone Treat Parkinson’s disease 2020 [29] Amisulpride Help prevent nausea and vomiting after surgery 2020 [30] Entities (NMEs) approved between 1994 and 6. Challenges of CADD 2014 from FDA’s drug database and Federal Although CADD has been making great Register (FR) [36]. The scientific data often contribution, it still faces many challenges. Its contain intellectually and mathematically algorithms should take into account the protein information, therefore there is a challenge flexibility. Nowadays, most CADD studies related to how to design data accessibly and assume a rigid protein structure which is not understandably to users [37]. This makes large accurate [31]. Study of Lexa et al. shows that scale virtual screening difficult. In addition, flexible docking can improve the prediction up many quality databases are commercial or to 80-95%, whereas the best performance of restricted, which means expensive or rigid docking only reaches 50% to 70% [32]. impossible to access from academia. This Another issue connects with false - positive challenge calls for an open access to chemical reports [33] which is likely associated with database, which is advocated by Irwin Lab and scoring function [34]. Shoichet Lab. Besides, nowadays big data has The second challenge concerns the encountered new infrastructure challenges such reliability and accessibility of database. as network resilience, network latency and Currently, the databases are fragmented, unpredictable behaviour in cloud - based coming from various sources and this can cause systems [38]. inconsistency [35] due to different enumeration The third challenge faced CADD is the standards. For example, Audibert et al. had complex biological system. CADD is expected detected that there is a considerable to describe effectively and accurately the inconsistency in reported data when they interactions of drugs with this system at collected IND dates for 587 New Molecule different levels from molecular, cellular, tissue
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