Identification of novel inhibitors against Mycobacterium tuberculosis l-alanine dehydrogenase (MTB-AlaDH) through structure-based virtual screening

Mycobacterium tuberculosis (MTB) the etiological agent of tuberculosis (TB) survives in the human host for decades evading the immune system in a latent or persistent state. The Rv2780 (ald) gene that codes for l-alanine dehydrogenase (l-AlaDH) enzyme catalyzes reversible oxidative deamination of l-alanine to pyruvate and is overexpressed under hypoxic and nutrient starvation conditions in MTB. At present, as there is no suitable drug available to treat dormant tuberculosis; it is essential to identify drug candidates that could potentially treat dormant TB. Availability of crystal structure of MTB l-AlaDH bound with co-factor NAD⁺ facilitated us to employ structure-based virtual screening approach to obtain new hits from a commercial library of Asinex database using energy-optimized pharmacophore modeling. The resulting pharmacophore consisted of three hydrogen bond donor sites (D) and two hydrogen bond acceptor sites (A). The database compounds with a fitness score more than 1.0 were further subjected to Glide high-throughput virtual screening and docking. Thus, we report the identification of best five hits based on structure-based design and their in vitro enzymatic inhibition studies revealed IC₅₀ values in the range of 35–80 μM.     

Structural requirements of 3-carboxyl-4(1H)-quinolones as potential antimalarials from 2D and 3D QSAR analysis

Malaria is a fatal tropical and subtropical disease caused by the protozoal species Plasmodium. Many commonly available antimalarial drugs and therapies are becoming ineffective because of the emergence of multidrug resistant Plasmodium falciparum, which drives the need for the development of new antimalarial drugs. Recently, a series of 3-carboxyl-4(1H)-quinolone analogs, derived from the famous compound endochin, were reported as promising candidates for orally efficacious antimalarials. In this study, to analyze the structure–activity relationships (SAR) of these quinolones and investigate the structural requirements for antimalarial activity, the 2D multiple linear regressions (MLR) method and 3D comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods are employed to evolve different QSAR models. All these models give satisfactory results with highly accurate fitting and strong external predictive abilities for chemicals not used in model development. Furthermore, the contour maps from 3D models can provide an intuitive understanding of the key structure features responsible for the antimalarial activities. In conclusion, we summarize the detailed position-specific structural requirements of these derivatives accordingly. All these results are helpful for the rational design of new compounds with higher antimalarial bioactivities.     

QSAR models for predicting cathepsin B inhibition by small molecules—Continuous and binary QSAR models to classify cathepsin B inhibition activities of small molecules

Cathepsin B is a potential target for the development of drugs to treat several important human diseases. A number of inhibitors targeting this protein have been developed in the past several years. Recently, a group of small molecules were identified to have inhibitory activity against cathepsin B through high throughput screening (HTS) tests. In this study, traditional continuous and binary QSAR models were built to classify the biological activities of previously identified compounds and to distinguish active compounds from inactive compounds for drug development based on the calculated molecular and physicochemical properties. Strong correlations were obtained for the continuous QSAR models with regression correlation coefficients (r²) and cross-validated correlation coefficients (q²) of 0.77 and 0.61 for all compounds, and 0.82 and 0.68 for the compound set excluding 3 outliers, respectively. The models were further validated through the leave-one-out (LOO) method and the training-test set method. The binary models demonstrated a strong level of predictability in distinguishing the active compounds from inactive compounds with accuracies of 0.89 and 0.94 for active and inactive compounds, respectively, in non-cross-validated models. Similar results were obtained for the cross-validated models. Collectively, these results demonstrate the models’ ability to discriminate between active and inactive compounds, suggesting that the models may be used to pre-screen compounds to facilitate compound optimization and to design novel inhibitors for drug development.     

酪氨酸激酶抑制剂的虚拟受体模型方法研究

利用柔性原子受体模型(FLARM)方法对一系列的异黄酮和喹诺酮衍生物表皮生长因子受体酪氨酸激酶抑制剂进行了三维定量构效关系研究,得到了合理的构效关系模型。FLARM方法的计算结果还给出了虚拟的受体模型,该模型说明了抑制剂与受体之间可能的相互作用。这些相互作用包括两个氢键和一个硫-芳香相互作用,以上结果仅仅是由7个化合物得到的。     

An investigation of structurally diverse carbamates for acetylcholinesterase (AChE) inhibition using 3D-QSAR analysis

In order to identify the essential structural features and physicochemical properties for acetylcholinesterase (AChE) inhibitory activity in some carbamate derivatives, the systematic QSAR (Quantitative Structure Activity Relationship) studies (CoMFA, advance CoMFA and CoMSIA) have been carried out on a series of (total 78 molecules) taking 52 and 26 molecules in training and test set, respectively. Statistically significant 3D-QSAR (three-dimensional Quantitative Structure Activity Relationship) models were developed on training set molecules using CoMFA and CoMSIA and validated against test set compounds. The highly predictive models (CoMFA q(2)=0.733, r(2)=0.967, predictive r(2)=0.732, CoMSIA q(2)=0.641, r(2)=0.936, predictive r(2)=0.812) well explained the variance in binding affinities both for the training and the test set compounds. The generated models suggest that steric, electrostatic and hydrophobic interactions play an important role in describing the variation in binding affinity. In particular the carbamoyl nitrogen should be more electropositive; substitutions on this nitrogen should have high steric bulk and hydrophobicity while the amino nitrogen should be electronegative in order to have better activity. These studies may provide important insights into structural variations leading to the development of novel AChE inhibitors which may be useful in the development of novel molecules for the treatment of Alzheimer's disease.     

表皮生长因子受体酪氨酸激酶抑制剂的药效团研究

根据一系列表皮生长因子受体酪氨酸激酶抑制剂的三维定量构效关系研究,得到了该类抑制剂的药效团,研究结果与Novartis的药效团模型相当类似。药效团包括一个氢键受体,一个氢键给体,一个疏水区和一个带有氯或溴原子的苯环。该药效团对于研究表皮生长因子受体酪氨酸激酶抑制剂结构与活性的关系具有重要的意义。通过三维数据库搜索可能会得到新的先导化合物。     

3D-QSAR and molecular docking studies of 1,3,5-triazene-2,4-diamine derivatives against r-RNA: novel bacterial translation inhibitors

Aminoglycoside mimetics inhibit bacterial translation by interfering with the ribosomal decoding site. To elucidate the structural properties of these compounds important for antibacterial activity, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were applied to a set of 56 aminoglycosides mimetics. The successful CoMFA model yielded the leave-one-out (LOO) cross-validated correlation coefficient (q(2)) of 0.708 and a non-cross-validated correlation coefficient (r(2)) of 0.967. CoMSIA model gave q(2)=0.556 and r(2)=0.935. The CoMFA and CoMSIA models were validated with 36 test set compounds and showed a good r(pred)(2) of 0.624 and 0.640, respectively. Contour maps of the two QSAR approaches show that electronic effects dominantly determine the binding affinities. These obtained results were agreed well with the experimental observations and docking studies. The results not only lead to a better understanding of structural requirements of bacterial translation inhibitors but also can help in the design of novel bacterial translation inhibitors.     

血管紧张素转化酶二肽抑制剂的构效关系

从肽链的一级结构出发,以分子电边矢量（molecular eleetro—negativity edge vector,MEEV）为参数,36种血管紧张素转化酶二肽抑制剂为样本,构建了血管紧张素转化酶二肽抑制剂的构效关系模型。通过模型分析得出二肽肽键的“二、五、七”键抑制酶活的规律,即：（1）肽键的羧基和Zn形成二配体,而肽键的N原子和羧基氧形成H键以稳定这一基团;（2）与ACE酶中Arg（Arginine,精氨酸）正电荷盐键作用的羧酸根和第二氨基酸的氨基之间形成的五键结构单元对其降压效果起关键作用;（3）含芳香族氨基酸的二肽抑制剂中的肽键的氨基和苯环部分羟基端呈反式构型,它们相隔7个键位。这一结构有利于分子间氢键的形成及保证抑制剂能稳定地和酶结合、结果表明：本模型有方法简单,能避免因为数据量的过大而引起的统计误差的优点,有望对血管紧张素肽类药物的台成及药物活性预测提供帮助.     

3-取代4-氧-3H-咪唑并[5,1-d][1,2,3,5]四嗪-8-羧酸衍生物抗肿瘤活性的定量构效关系研究

目的:研究3-取代4-氧-3H-咪唑并[5,1-d][1,2,3,5]四嗪-8-羧酸衍生物分子结构与抗肿瘤活性的关系.方法:采用量子化学和分子力学方法计算分子结构参数,利用Cram-Schmidt正交化法筛选参数,利用偏最小二乘法建立QsAR模型.结果:建立合理的3-取代-4.氧-3H-咪唑并[5,1-d][1,2,3,5]四嗪-8-羧酸衍生物抗肿瘤活性模型.结论:3-取代-4-氧-3H-咪唑并[5,1-d][1,2,3,5]四嗪-8-羧酸衍生物抗肿瘤活性与分子油水分配系数LogP和8位取代基R1上的非氢原子净电荷Q1相关,研究结果可为同类抗肿瘤药物的分子设计提供参考.     

The role of LasR active site amino acids in the interaction with the Acyl Homoserine Lactones (AHLs) analogues: A computational study

The present work combines molecular docking calculations, 3D-QSAR, molecular dynamics simulations and free binding energy calculations (MM/PBSA and MM/GBSA) in a set of 28 structural analogues of acyl homoserine lactones with Quorum Sensing antagonist activity. The aim of this work is to understand how ligand binds and is affected by the molecular microenvironment in the active site of the LasR receptor for pseudomonas aeruginosa. We also study the stability of the interaction to find key structural characteristics that explain the antagonist activities of this set of ligands. This information is relevant for the rational modification or design of molecules and their identification as powerful LasR modulators.The analysis of molecular docking simulations shows that the 28 analogues have a similar binding mode compared to the native ligand. The carbonyl groups belonging to the lactone ring and the amide group of the acyl chain are oriented towards the amino acids forming hydrogen bond like interactions. The difference in antagonist activity is due to location and orientation of the LasR side chains within the hydrophobic pocket in its binding site. Additionally, we carried out molecular dynamics simulations to understand the conformational changes in the ligand-receptor interaction and the stability of each complex. Results show a direct relationship among the interaction energies of the ligands and the activities as an antagonist of the LasR receptor.     

Identification of Mycobacterium tuberculosis enoyl-acyl carrier protein reductase inhibitors: A combined in-silico and in-vitro analysis

Mycobacterium tuberculosis (Mtb), had developed evolutionary changes in its genome to adapt for survival and thereby generated multi-drug resistant strains. However, novel drug targets that remained unchanged for their biochemical role has impressed the research community to target such proteins. The comprehensive analysis of multiple protein targets has influenced us to make a consensus structural rule exploited by pharmacophore and other allied techniques from a large repository of protein structures. In this pursuit, we made a retrospective analysis of pharmacophores mapped from the tuberculosis structural proteome and identified unique patterns that can be employed for the novel molecules design. The current work on NADH–dependent enoyl–acyl carrier protein reductase (InhA) has yielded top scored pharmacophore models which were searched over SPECS natural product database to prioritize the molecules that can be targeted against Mtb. With efforts on rigorous validation and expertise, we have identified such pharmacophoric patterns from natural compounds that can be used as initial hits. Subsequently, these hits were subjected to in-vitro antitubercular evaluation to ensure the inhibitory activity against the mycobacterium culture growth (MtbH37Rv). Furthermore, docking simulations were carried out to provide an insight on the possible modes of interaction between the experimentally explored compounds and InhA.     

主成分分析-神经网络方法用于硝基苯及其同系物的QSAR研究

运用混合密度泛函理论DFT-B3LYP,以6-31G＊为基组计算35个硝基苯及其同系物电子结构的量化参数,采用主成分分析法对16个量化参数进行预处理,并结合人工神经网络对硝基苯及其同系物的QSAR进行了研究。35个化合物被随机分为两组,即训练集和测试集,其RMS值分别为0．095和0．111。取得了较满意的结果。     

Sub-microliter scale in-gel loop-mediated isothermal amplification (LAMP) for detection of Mycobacterium tuberculosis

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is a common human disease that is prevalent in resource-deprived areas of the world. Current detection techniques for TB require expensive conventional instruments in a laboratory setting, preventing accessible and low cost diagnosis of the disease. Using a loop-mediated isothermal amplification (LAMP) assay, we have amplified and detected TB in a 6 × 8 semisolid polyacrylamide gel post array using an inexpensive prototype instrument. Each post contains 670 nL of volume, minimizing the need for large quantities of reagents. Amplified DNA is detected via fluorescence of the dye LCGreen Plus+, which is polymerized into the gel along with other reagents. The prototype device contains a Peltier element for heating, a diode laser as an excitation source, and a CCD camera for detecting fluorescence in real-time. About 12 Mycobacterium tuberculosis genomes per gel post can be detected within 75 min of amplification. This sensitivity is similar to that obtained by conventional methods using a commercial thermocycler. We achieved comparable LAMP amplification when the template is added externally or when the template is polymerized in the gel. This rapid isothermal amplification technology, with its simple thermal requirements, has the potential to be integrated into micro-devices and serves as a model for implementing future low-cost point of care diagnostics.