Robust design of some selective matrix metalloproteinase-2 inhibitors over matrix metalloproteinase-9 through in silico/fragment-based lead identification and de novo lead modification: Syntheses and biological assays

Derivatives of D(-) glutamine-based MMP-2 inhibitors as an effective remedy for the management of chronic myeloid leukemia-Part-I: Synthesis, biological screening and in silico binding interaction analysis

Chronic myeloid leukemia (CML) is a global issue and the available drugs such as tyrosine kinase inhibitors (TKIs) comprise various toxic effects as well as resistance and cross-resistance. Therefore, novel molecules targeting specific enzymes may unravel a new direction in antileukemic drug discovery. In this context, targeting gelatinases (MMP-2 and MMP-9) can be an alternative option for the development of novel molecules effective against CML. In this article, some D(-)glutamine derivatives were synthesized and evaluated through cell-based antileukemic assays and tested against gelatinases. The lead compounds, i.e., benzyl analogs exerted the most promising antileukemic potential showing nontoxicity in normal cell line including efficacious gelatinase inhibition. Both these lead molecules yielded effective apoptosis and displayed marked reductions in MMP-2 expression in the K562 cell line. Not only that, but both of them also revealed effective antiangiogenic efficacy. Importantly, the most potent MMP-2 inhibitor, i.e., benzyl derivative of p-tosyl D(-)glutamine disclosed stable binding interaction at the MMP-2 active site correlating with the highly effective MMP-2 inhibitory activity. Therefore, such D(-)glutamine derivatives might be explored further as promising MMP-2 inhibitors with efficacious antileukemic profiles for the treatment of CML in the future.

Synthesis and SAR investigation of biphenylaminoquinoline derivatives with benzyloxy substituents as promising anticancer agents

The biphenyl scaffold represents a prominent privileged structure within the realms of organic chemistry and drug development. Biphenyl derivatives have demonstrated notable biological activities, including antimicrobial, anti-inflammatory, anti-HIV, and the treatment of neuropathic pain. Importantly, their anticancer abilities should not be underestimated. In this context, the present study involves the design and synthesis of a series of biphenyl derivatives featuring an additional privileged structure, namely the quinoline core. We have also diversified the substituents attached to the benzyloxy group at either the meta or para position of the biphenyl ring categorized into two distinct groups: [4,3']biphenylaminoquinoline-substituted and [3,3']biphenylaminoquinoline-substituted compounds. We embarked on an assessment of the cytotoxic activities of these derivatives in colorectal cancer cell line SW480 and prostate cancer cell line DU145 for exploring the structure-activity relationship. Furthermore, we determined the IC50 values of selected compounds that exhibited superior inhibitory effects on cell viability against SW480, DU145 cells, as well as MDA-MB-231 and MiaPaCa-2 cells. Notably, [3,3']biphenylaminoquinoline derivative 7j displayed the most potent cytotoxicity against these four cancer cell lines, SW480, DU145, MDA-MB-231, and MiaPaCa-2, with IC50 values of 1.05 μM, 0.98 μM, 0.38 μM, and 0.17 μM, respectively. This highly promising outcome underscores the potential of [3,3']biphenylaminoquinoline 7j for further investigation as a prospective anticancer agent in future research endeavors.

Small molecular exogenous modulators of active forms of MMPs

Matrix metalloproteinases (MMPs) are endopeptidases, and their activity depends on calcium and zinc metal ions. These enzymes are expressed originally in zymogenic form, where the active site of proteins is closed by a prodomain which is removed during activation. A homeostatic balance of their activity is primarily regulated by a 'cysteine switch' located on a consensus sequence of the prodomain and natural endogenous inhibitors, called tissue inhibitors of metalloproteinases (TIMPs). Breakage of this homeostasis may lead to various pathological conditions, which may require further activation and/or inhibition of these enzymes to regenerate that balance. Here, we report four modulators, more specifically, three inhibitors (I1, I2 and I3), and one exogenous activator (L) of the active form of human collagenase MMP-1 (without prodomain). The results were confirmed by binding studies using fluorescence-based enzyme assays.

Assessing structural insights into in-house arylsulfonyl L-(+) glutamine MMP-2 inhibitors as promising anticancer agents through structure-based computational modelling approaches

MMP-2 is potentially contributing to several cancer progressions including leukaemias. Therefore, considering MMP-2 as a promising target, novel anticancer compounds may be designed. Here, 32 in-house arylsulfonyl L-(+) glutamines were subjected to various structure-based computational modelling approaches to recognize crucial structural attributes along with the spatial orientation for higher MMP-2 inhibition. Again, the docking-based 2D-QSAR study revealed that the Coulomb energy conferred by Tyr142 and total interaction energy conferred by Ala84 was crucial for MMP-2 inhibition. Importantly, the docking-dependent CoMFA and CoMSIA study revealed the importance of favourable steric, electrostatic, and hydrophobic substituents at the terminal phenyl ring. The MD simulation study revealed a lower fluctuation in the RMSD, RMSF, and Rg values indicating stable binding interactions of MMP-2 and these molecules. Moreover, the residual hydrogen bond and their interaction analysis disclosed crucial amino acid residues responsible for forming potential hydrogen bonding for higher MMP-2 inhibition. The results can effectively aid in the design and discovery of promising small-molecule drug-like MMP-2 inhibitors with greater anticancer potential in the future.

Novel Matrix Metalloproteinase-9 (MMP-9) Inhibitors in Cancer Treatment

Matrix metalloproteinases (MMPs) belong to a family of zinc-dependent proteolytic metalloenzymes. MMP-9, a member of the gelatinase B family, is characterized as one of the most intricate MMPs. The crucial involvement of MMP-9 in extracellular matrix (ECM) remodeling underscores its significant correlation with each stage of cancer pathogenesis and progression. The design and synthesis of MMP-9 inhibitors is a potentially attractive research area. Unfortunately, to date, there is no effective MMP-9 inhibitor that passes the clinical trials and is approved by the FDA. This review primarily focuses on exploring the diverse strategies employed in the design and advancement of MMP-9 inhibitors, along with their anticancer effects and selectivity. To illuminate the essential structural characteristics necessary for the future design of novel MMP-9 inhibitors, the current narrative review highlights several recently discovered MMP-9 inhibitors exhibiting notable selectivity and potency.

Discovery of TP0597850: A Selective, Chemically Stable, and Slow Tight-Binding Matrix Metalloproteinase-2 Inhibitor with a Phenylbenzamide-Pentapeptide Hybrid Scaffold

Matrix metalloproteinase-2 (MMP2) is a zinc-dependent endopeptidase and a promising target for various diseases, including cancer and fibrosis. Herein, we report the discovery of a novel MMP2-selective inhibitor with high chemical stability and slow tight-binding features. Based on the degradation mechanism of our small-molecule-peptide hybrid 1, the tripeptide linker {5-aminopentanoic acid [Ape(5)]-Glu-Asp} of 1 was replaced by a shorter linker (γ-D-Glu). Phenylbenzamide was suitable for the new generation of MMP2 inhibitors as an S1' pocket-binding group. The introduction of (4S)-aminoproline dramatically increased the chemical stability while maintaining high subtype selectivity because of its interaction with Glu130. TP0597850 (18) exhibited high stability over a wide range of pH values as well as potent MMP2 inhibition (K_i = 0.034 nM) and ≥2000-fold selectivity determined using the inhibition constants. A kinetic analysis revealed that it possesses slow tight-binding nature with a long MMP2 dissociative half-life (t_1/2 = 265 min).

Selective Inhibitors of Medium-Size S1' Pocket Matrix Metalloproteinases: A Stepping Stone of Future Drug Discovery

Among various matrix metalloproteinases (MMPs), MMPs having medium-size S1' pockets are established as promising biomolecular targets for executing crucial roles in cancer, cardiovascular diseases, and neurodegenerative diseases. However, no such MMP inhibitors (MMPIs) are available to date as drug candidates despite a lot of continuous research work for more than three decades. Due to a high degree of structural resemblance among these MMPs, designing selective MMPIs is quite challenging. However, the variability and uniqueness of the S1' pockets of these MMPs make them promising targets for designing selective MMPIs. In this perspective, the overall structural aspects of medium-size S1' pocket MMPs including the unique binding patterns of enzyme-inhibitor interactions have been discussed in detail to acquire knowledge regarding selective inhibitor designing. This overall knowledge will surely be a curtain raiser for the designing of selective MMPIs as drug candidates in the future.

Insight into the structural requirements of gelatinases (MMP-2 and MMP-9) inhibitors by multiple validated molecular modelling approaches: Part II

Inhibition of the matrix metalloproteinases (MMPs) is effective against metastasis of secondary tumours. Previous MMP inhibitors have failed in clinical trials due to their off-target toxicity in solid tumours. Thus, newer MMP inhibitors now have paramount importance. Here, different molecular modelling techniques were applied on a dataset of 110 gelatinase (MMP-2 and MMP-9) inhibitors. The objectives of the present study were to identify structural fingerprints for gelatinase inhibition and also to develop statistically validated QSAR models for the screening and prediction of different derivatives as MMP-2 (gelatinase A) and MMP-9 (gelatinase B) inhibitors. The Bayesian classification study provided the ROC values for the training set of 0.837 and 0.815 for MMP-2 and MMP-9, respectively. The linear model also produced the leave-one-out cross-validated Q² of 0.805 (eq. 1, MMP-2) and 0.724 (eq. 2, MMP-9), an r² of 0.845 (eq. 1, MMP-2) and 0.782 (eq. 2, MMP-9), an r²_Pred of 0.806 (eq. 1, MMP-2) and 0.732 (eq. 2, MMP-9). Similarly, non-linear learning models were also statistically significant and reliable. Overall, this study may help in the rational design of newer compounds with higher gelatinase inhibition to fight against both primary and secondary cancers in future.

Applying comparative molecular modelling techniques on diverse hydroxamate-based HDAC2 inhibitors: an attempt to identify promising structural features for potent HDAC2 inhibition

Histone deacetylase 2 (HDAC2) has been implicated in a variety of cardiovascular and neurodegenerative disorders as well as in cancers. Thus, HDAC2 has become an exclusive target for anticancer drug development. Therefore, the development of newer HDAC2 inhibitors in disease conditions is a prime goal to restrain such a scenario. Although a handful of HDAC inhibitors was accepted for the treatment of HDAC-related disease conditions, the non-selective nature of these entities is one of the major setbacks in the treatment of specific HDAC isoform-related pathophysiology. In this framework, the analyses of pre-existing molecules are essential to identify the important structural features that can fulfil the requirements for the cap and linker moieties to obtain potent and effective HDAC2 inhibition. Thus, in this study, the implementation of a combined comparative 2D and 3D molecular modelling techniques was done on a group of 92 diverse hydroxamate derivatives having a wide range of HDAC2 inhibitory potency. Besides other crucial features, this study upheld the importance of groups like triazole and benzyl moieties along with the molecular fields that are crucial for regulating HDAC2 inhibition. The outcomes of this study may be employed for the designing of HDAC2 inhibitors in future.

Synthesis, anticancer activity, SAR and binding mode of interaction studies of substituted pentanoic acids: part II

Aim: Our previous results suggest that phenyl/naphthylacetyl pentanoic acid derivatives may exhibit dual MMP-2 and HDAC8 inhibitory activities and show effective cytotoxic properties. Methodology: Here, 13 new compounds (C1-C13) were synthesized and characterized. Along with these new compounds, 16 previously reported phenyl/napthylacetyl pentanoic acid derivatives (C14-C29) were biologically evaluated. Results: Compounds C6 and C27 showed good cytotoxicity against leukemia cell line Jurkat E6.1. The mechanisms of cytotoxicity of these compounds were confirmed by DNA deformation assay and reactive oxygen species assay. MMP-2 and HDAC8 expression assays suggested the dual inhibiting property of these two compounds. These findings were supported by results of molecular docking studies. In silico pharmacokinetic properties showed compounds C6 and C27 have high gastrointestinal absorption. Conclusion: This study highlights the action of phenyl/naphthylacetyl pentanoic acid derivatives as anticancer agents.

Ligand-based design of anticancer MMP2 inhibitors: a review

MMP2, a Zn²⁺-dependent metalloproteinase, is related to cancer and angiogenesis. Inhibition of this enzyme might result in a potential antimetastatic drug to leverage the anticancer drug armory. In silico or computer-aided ligand-based drug design is a method of rational drug design that takes multiple chemometrics (i.e., multi-quantitative structure-activity relationship methods) into account for virtually selecting or developing a series of probable selective MMP2 inhibitors. Though existing matrix metalloproteinase inhibitors have shown plausible pan-matrix metalloproteinase (MMP) activity, they have resulted in various adverse effects leading to their being rescinded in later phases of clinical trials. Therefore a review of the ligand-based designing methods of MMP2 inhibitors would result in an explicit route map toward successfully designing and synthesizing novel and selective MMP2 inhibitors.

A robust classification-dependent multi-molecular modelling study on some biphenyl sulphonamide based MMP-8 inhibitors

Matrix metalloproteinases (MMPs) are a group of zinc and calcium-dependent endopeptidases, which contribute to different physiological and biological activities via extracellular matrix (ECM) degradation. Matrix metalloproteinase-8 (MMP-8) belongs to type-II collagenases of the MMP family that has contribution in several physiological disorders such as cardiovascular diseases, joint, renal, digestive and respiratory disorders as well as in cancer. In clinical study, MMP-8 is found to be associated with periodontal disease condition. Therefore, MMP-8 specific inhibitors should be developed to target these disorders. The biphenyl sulphonamide (BPS) moiety is one of the crucial structural characteristics found in several MMP-8 inhibitors. Here, different classification-based molecular modelling methods were used to explore the structural features that lead to the activity variation of a series of MMP-8 inhibitors possessing a BPS moiety. Our current classification-based structural analysis of these BPS-derived MMP-8 inhibitors was able to identify the importance of several structural features such as the tetrahydroisoquinoline and N-Boc pyridyl groups, which have positive influences on MMP-8 inhibition. This study was also reflected the importance of the zinc-binding groups (ZBGs) like the hydroxamate and phosphonate for potent and sub-nanomolar range MMP-8 inhibition, which may benefit the development of highly potent MMP-8 inhibitors.

Insight into the structural requirement of aryl sulphonamide based gelatinases (MMP-2 and MMP-9) inhibitors - Part I: 2D-QSAR, 3D-QSAR topomer CoMFA and Naïve Bayes studies - First report of 3D-QSAR Topomer CoMFA analysis for MMP-9 inhibitors and jointly inhibitors of gelatinases together

Gelatinases [gelatinase A - matrix metalloproteinase-2 (MMP-2), gelatinase B - matrix metalloproteinase-9 (MMP-9)] play key roles in many disease conditions including cancer. Despite some research work on gelatinases inhibitors both jointly and individually had been reported, challenges still exist in achieving potency as well as selectivity. Here in part I of a series of work, we have reported the structural requirement of some arylsulfonamides. In particular, regression-based 2D-QSARs, topomer CoMFA (comparative molecular field analysis) and Bayesian classification models were constructed to refine structural features for attaining better gelatinase inhibitory activity. The 2D-QSAR models exhibited good statistical significance. The descriptors nsssN, SHBint6, SHBint7, PubchemFP629 were directly correlated with the MMP-2 binding affinities whereas nsssN, SHBint10 and AATS2i were directly proportional to MMP-9 binding affinities. The topomer CoMFA results indicated that the steric and electrostatic fields play key roles in gelatinase inhibition. The established Naïve Bayes prediction models were evaluated by fivefold cross validation and an external test set. Furthermore, important molecular descriptors related to MMP-2 and MMP-9 binding affinities and some active/inactive fragments were identified. Thus, these observations may be helpful for further work of aryl sulphonamide based gelatinase inhibitors in future.

Inhibitors of gelatinases (MMP-2 and MMP-9) for the management of hematological malignancies

Matrix metalloproteinase-2 (MMP-2) and matrix metalloproteinase-9 (MMP-9) are collectively known as gelatinases whereas MMP-2 is gelatinase-A and MMP-9 is termed as gelatinase-B. Gelatinases and other matrix metalloproteinases (MMPs) have long been associated with solid tumor invasion, metastasis and angiogenesis. However, there is paucity of data available regarding the role of gelatinases in hematological malignancies. Recent studies have shown that gelatinases activities or functions are correlated with hematological malignancies. Strategies for designing more specific gelatinase inhibitors like catalytic (CAT) domain inhibitors and hemopexin (PEX) domain inhibitors as well as signaling pathway based or gelatinase expression inhibitors had been reported against hematologic malignant cells. Several substrate based non-selective to non-substrate based relatively selective synthetic matrix metalloproteinase inhibitors (MMPIs) had been developed. Few MMPIs had reached in clinical trials during the period of 1990s-2000s. Unfortunately the anti-tumor and anti-metastatic efficacies of these MMPIs were not justified with patients having several advanced stage solid tumor cancers in any substantial number of clinical trials. Till date not a single MMPI passed phase III clinical trials designed for advanced metastatic cancers due to adverse events as well as lack of ability to show uniformity in disease prolongation. With the best of our knowledge no clinical trial study has been reported with small molecule synthetic inhibitors against hematological malignancies. This review looks at the outcome of clinical trials of MMPIs for advanced stage solid tumors. This can therefore, act as a learning experience for future development of successful gelatinase inhibitors for the management of hematological malignancies.

Quantitative activity–activity relationship (QAAR) driven design to develop hydroxamate derivatives of pentanoic acids as selective HDAC8 inhibitors: synthesis, biological evaluation and binding mode of interaction studies

Histone deacetylase 8 (HDAC8) has been implicated as a potential drug target of many diseases including cancer.

Outline of gelatinase inhibitors as anti-cancer agents: A patent mini-review for 2010-present

Matrix metalloproteinases (MMPs) are involved in several pathological and physiological functions. Gelatinases (MMP-2 and -9) have significant attention as therapeutic targets against cancer. Gelatinase inhibitors have demonstrated their effectiveness in several diseases including cancer. However, it is quite a challenging task to develop inhibitors as a therapeutic agent. This review summarizes the patent dedicated to the medicinal chemistry of gelatinase inhibitor reported over last decades. We examine the patent being pursued for gelatinase inhibitor development to highlight the key issues. The main aim is to provide the scientific community with an overview of the patented gelatinase inhibitors to allow further development. During early 2000s, some MMP inhibitors failed to pass the clinical trials. Hence, the lessons learned from early evidence and recent knowledge in that field will rejuvenate the development of selective inhibitors. Various studies and patents have continued in the recent years to expand knowledge. Continuously, our research team has been involved in the design of potent and selective gelatinase inhibitors for the past few years. This study is a part of our efforts. This study may be beneficial in the design and development of better gelatinase inhibitors in the future.

N-Sulfonyl dipeptide nitriles as inhibitors of human cathepsin S: In silico design, synthesis and biochemical characterization

A library of cathepsin S inhibitors of the dipeptide nitrile chemotype, bearing a bioisosteric sulfonamide moiety, was synthesized. Kinetic investigations were performed at four human cysteine proteases, i.e. cathepsins S, B, K and L. Compound 12 with a terminal 3-biphenyl sulfonamide substituent was the most potent (K_i = 4.02 nM; selectivity ratio cathepsin S/K = 5.8; S/L = 67) and 24 with a 4'-fluoro-4-biphenyl sulfonamide substituent the most selective cathepsin S inhibitor (K_i = 35.5 nM; selectivity ratio cathepsin S/K = 57; S/L = 31). In silico design and biochemical evaluation emphasized the impact of the sulfonamide linkage on selectivity and a possible switch of P2 and P3 substituents with respect to the occupation of the corresponding binding sites of cathepsin S.

Chemical-informatics approach to COVID-19 drug discovery: Monte Carlo based QSAR, virtual screening and molecular docking study of some in-house molecules as papain-like protease (PLpro) inhibitors

World Health Organization characterized novel coronavirus disease (COVID-19), caused by severe acute respiratory syndrome (SARS) coronavirus-2 (SARS-CoV-2) as world pandemic. This infection has been spreading alarmingly by causing huge social and economic disruption. In order to response quickly, the inhibitors already designed against different targets of previous human coronavirus infections will be a great starting point for anti-SARS-CoV-2 inhibitors. In this study, our approach integrates different ligand based drug design strategies of some in-house chemicals. The study design was composed of some major aspects: (a) classification QSAR based data mining of diverse SARS-CoV papain-like protease (PLpro) inhibitors, (b) QSAR based virtual screening (VS) to identify in-house molecules that could be effective against putative target SARS-CoV PLpro and (c) finally validation of hits through receptor-ligand interaction analysis. This approach could be used to aid in the process of COVID-19 drug discovery. It will introduce key concepts, set the stage for QSAR based screening of active molecules against putative SARS-CoV-2 PLpro enzyme. Moreover, the QSAR models reported here would be of further use to screen large database. This study will assume that the reader is approaching the field of QSAR and molecular docking based drug discovery against SARS-CoV-2 PLpro with little prior knowledge.

Communicated by Ramaswamy H. Sarma

Matrix metalloproteinase-9 (MMP-9) and its inhibitors in cancer: A minireview

Matrix metalloproteinases (MMPs) are zinc dependent proteolytic metalloenzyme. MMP-9 is one of the most complex forms of matrix metalloproteinases. MMP-9 has the ability to degrade the extracellular matrix (ECM) components and has important role in the pathophysiological functions. Overexpression and dysregulation of MMP-9 is associated with various diseases. Thus, regulation and inhibition of MMP-9 is an important therapeutic approach for combating various diseases including cancer. Inhibitors of MMP-9 can be used as anticancer agents. Till date no selective MMP-9 inhibitors passed the clinical trials. In this review the structure, activation, function and inhibitors of MMP-9 are mainly focused. Some highly active and/or selective MMP-9 inhibitors have been discussed which may be helpful to explore the structural significance of MMP-9 inhibitors. This study may be useful to design new potent and selective MMP-9 inhibitors against cancer in future.

Anin silicoperception for newly isolated flavonoids from peach fruit as privileged avenue for a countermeasure outbreak of COVID-19

3′-Hydroxy-4′-methoxy-chroman-7-O-β-d-glucopyranoside 4 was first isolated from a natural source, together with three known compounds, the ferulic acid heptyl ester 1, naringenin 2, and 4,2′,4′-trihydroxy-6′-methoxychalcone-4′-O-β-d-glucopyranoside 3, which were isolated from peach [Prunus persica (L.) Batsch] fruits. These compounds were subjected to different virtual screening strategies in order to examine their activity to combat the COVID-19 outbreak. The study design composed of some major aspects: (a) docking with main protease (M^pro), (b) docking with spike protein, (c) 3D shape similarity study (Rapid Overlay Chemical Similarity-ROCS) to the clinically used drugs in COVID-19 patients, and finally, (d) the rule of five and the estimated pre-ADMT properties of the separated flavonoids. Docking study with M^pro of SARS-CoV-2 (PDB ID:6LU7, and 6Y2F) showed that compound 3, its aglycone part, and compound 4 have a strong binding mode to a protease receptor with key amino acids, especially Gln:166AA, and having a similar docking pose to co-crystalized ligands. Docking with the spike protein of SARS-CoV-2 illustrated that compounds 3 and 4 have a good binding affinity to PDB ID:6VSB through the formation of HBs with Asp:467A and Asn:422A. According to ROCS analysis, compounds 1, 3, and 4 displayed high similarities to drugs that prevent SARS-Co2 entry to the lung cells or block the inflammatory storm causing lung injury. Compounds 3 and 4 are good candidates for drug development especially because they showed predicted activity against SARS-CoV-2 through different mechanisms either by preventing genome replication or by blocking inflammatory storm that trigger lung injury. These compounds were isolated from peach fruit, and the study supports data and continues with the recommendation of peach fruits in controlling and managing COVID-19 cases.

3′-Hydroxy-4′-methoxy-chroman-7-O-β-d-glucopyranoside 4, together with three known compounds, ferulic acid heptyl ester 1, naringenin 2, and 4,2′,4′-trihydroxy-6′-methoxychalcone-4′-O-β-d-glucopyranoside 3, was isolated from peach fruits.

Synthesis, anticancer activity, structure–activity relationship and binding mode of interaction studies of substituted pentanoic acids

Aim: Simultaneous inhibition of MMP-2 and HDAC8 may be an effective strategy to target cancer. Methodology: In continuation of our earlier efforts, a series of substituted pentanoic acids (1–18) were synthesized and checked for their biological activity along with some earlier reported compounds (19 –35). Results: Compounds 18 and 31 were found to induce apoptosis effectively in a dose-dependent fashion in Jurkat-E6.1 cell line. They reduced the expression of both MMP-2 and HDAC8 effectively. 31 also produced prominent intensity of fluorescence to bring nick in Jurkat-E6.1 cells. 31 also showed cellular arrest in sub-G0 phase. Conclusion: Such compounds may be useful to battle against cancer.

Automated De Novo Drug Design: Are We Nearly There Yet?

Medicinal chemistry and, in particular, drug design have often been perceived as more of an art than a science. The many unknowns of human disease and the sheer complexity of chemical space render decision making in medicinal chemistry exceptionally demanding. Computational models can assist the medicinal chemist in this endeavour. Provided here is an overview of recent examples of automated de novo molecular design, a discussion of the concepts and computational approaches involved, and the daring prediction of some of the possibilities and limitations of drug design using machine intelligence.

QSAR modelling on a series of arylsulfonamide-based hydroxamates as potent MMP-2 inhibitors

Matrix metalloproteinase-2 (MMP-2) is a lucrative therapeutic target as far as anticancer drug discovery is concerned. Overexpression of MMP-2 is found to facilitate tumour propagation through the involvement of vascular endothelial growth factor (VEGF). However, even after different techniques, finding a target-specific MMP-2 inhibitor with respectable pharmacodynamic properties is still a challenging task. Regression-dependent quantitative structure-activity relationship (QSAR) strategies might be among the possible drug design methods to explore the essential structural features that would be valuable to find a suitable MMP-2 inhibitor. In this paper, 72 molecules were explored using the PaDEL descriptors and stepwise multiple linear regression (S-MLR). The partial least squares (PLS) method was also used to create a viable statistical model with an acceptable metric related to these models. The final statistical models were formed with statistical parameters within acceptable range (r² = 0.797, Q² = 0.725 and r²_pred = 0.643 for the MLR model, and r² = 0.780, Q² = 0.685 and r²_pred = 0.666 for the PLS model). The models were analysed and compared with those already published on the same endpoint.

First Report on the Validated Classification-Based Chemometric Modeling of Human Rhinovirus 3C Protease (HRV 3Cpro) Inhibitors

Human rhinoviruses (HRVs), a major cause of common cold and upper respiratory infections, may trigger severe respiratory complications like asthma and COPD. To date, no drugs are available in the market which are designed as novel HRV inhibitors despite the involvement of some pharmaceutical companies' due to economical and clinical constraints. HRV 3C protease may be a potential target for drug design as it plays crucial role in viral RNA replication and virion assembly process. Therefore, designing novel HRV 3Cpro inhibitors is necessary and demanding in the field of antiviral drug design. In this article, statistically significant and validated classification-based QSARs of a series of HRV 3Cpro inhibitors were performed for the first time as per the authors' knowledge. Results suggest that oxopyrrolidine and piperidinone rings are favored whereas carboxybenzyl and unsubstituted benzyl functions may be unfavorable. Moreover, this group, along with cyclic alkyl or aryl ring structures may favor HRV 3Cpro inhibition. These observations may be utilized for the design of a higher active anti-HRV agent in future.

Biomolecular basis of matrix metallo proteinase-9 activity

Matrix metalloproteinases (MMPs) are structurally related endopeptidases. They are also known as metzincins due to their interaction with zinc ion of the conserved methionine (Met) at the active site. MMPs play an important role in physiological and signaling processes of wound healing, bone resorption and angiogenesis. The structure of MMPs consists of signal peptide, propeptide, catalytic domain, hinge region and hemopexin-like domain. MMP-9 shares high structural and functional similarities with MMP-2, therefore designing selective MMP-9 inhibitors (MMPIs) is challenging. The selectivity can be achieved by targeting S2 subsite of MMP-9 that is having difference with MMP-2. Further, targeting its exosite and protein disulfide isomerase may also provide selective MMPIs. The review highlights the molecular features and basis of MMP-9 enzyme action. The MMPIs reported in the recent years have also been included.

Multiple molecular modelling studies on some derivatives and analogues of glutamic acid as matrix metalloproteinase-2 inhibitors

Matrix metalloproteinase-2 (MMP-2) is a potential target in anticancer drug discovery due to its association with angiogenesis, metastasis and tumour progression. In this study, 67 glutamic acid derivatives, synthesized and evaluated as MMP-2 inhibitors, were taken into account for multi-QSAR modelling study (regression-based 2D-QSAR, classification-based LDA-QSAR, Bayesian classification QSAR, HQSAR, 3D-QSAR CoMFA and CoMSIA as well as Open3DQSAR). All these QSAR studies were statistically validated individually. Regarding the 3D-QSAR analysis, the Open3DQSAR results were better than CoMFA and CoMSIA, although all these 3D-QSAR models supported each other. The importance of biphenylsulphonyl moiety over phenylacetyl/naphthylacetyl moieties was established due to its association with favourable steric and hydrophobic characters. HQSAR, LDA-QSAR and Bayesian classification QSAR studies also suggested that the biphenylsulphonamido group was better than the phenylacetylcarboxamido function. Additionally, glutamines were proven to be far better inhibitors than isoglutamines. Observations obtained from the current study were revalidated and supported by the earlier reported molecular modelling studies. Depending on these observations, newer glutamic acid-based compounds may be designed further in future for potent MMP-2 inhibitory activity.

Benzamide porphyrins with directly conjugated and distal pyridyl or pyridinium groups substituted to the porphyrin macrocycles: Study of the photosensitising abilities as inducers of apoptosis in cancer cells under photodynamic conditions

Amphiphilic porphyrin photosensitisers (PSs) having combinations of directly substituted pyridyl group(s) at the meso-position of a porphyrin macrocycle, and/or indirectly linked pyridyl groups as benzamide derivatives are reported. The compounds 5,10,15,20-tetrakis-(4-pyridylbenzamide)porphyrin (A.2), 5,10,15,20-tetra[N-(pyridine-4-yl)benzamidium] porphyrin (A.3), 5-mono-(4-pyridyl)-10,15,20-tris-(4-pyridylbenzamide)porphyrin (B.2) and 5-mono-(4-methylpyridinium)-10,15,20-tris-(4-pyridiniumbenzamide)porphyrin (B.3) were synthesised. The compounds were successfully characterised through UV-Vis, Emission, ¹H NMR, and ESI-HRMS techniques. To evaluate the effect of this combination of directly conjugated and non-conjugated pyridyl/cationic pyridinium groups on the porphyrin macrocycle, the efficacy of the synthesised compounds was compared to a known standard 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin (TMPyP). These compounds show better efficacy (IC₅₀'s ranging between 0.66±0.04μM to 3.71±1.01μM) against A549 (human epithelial adenocarcinoma lung cancer) cell line under in vitro photodynamic conditions in comparison to MDA-MB-231 (breast cancer) (IC₅₀'s ranging between 3.7±0.087μM to 12.1±0.12μM) and Pa-1 (ovarian cancer) (IC₅₀'s ranging between 17.9±0.01μM to 42.45±0.02μM) cell lines. It was found that B.3, having a pyridinium group attached to the meso-position of the macrocycle along with three distal cationic pyridinium groups, independent of the porphyrinic electron delocalisation cycle, showed better photocytotoxic efficacy (IC₅₀=0.66±0.04μM, A549 lung cancer cell line) and higher potential to promote apoptosis and hence better efficacy as PS towards cancer photodynamic therapy (PDT). The PDT activity of B.3 was further verified and established by various biological assays, viz. Annexin V assay, cell cycle assay, and reactive oxygen species (ROS) activity assay.

Recent opportunities in matrix metalloproteinase inhibitor drug design for cancer

INTRODUCTION

The overexpression of matrix metalloproteinase (MMP) plays an important role in the context of tumor invasion and metastasis, and MMP-2 has been characterized as the most validated target for cancer. Therefore, it is necessary to design matrix metalloproteinase inhibitors (MMPIs) that would be active and selective against MMP-2 but non-selective toward other MMPs. Areas covered: This article clearly describes the structural character of MMP-2 followed by a review of the recent development of selective MMP-2 inhibitors based on their basic structures. Expert opinion: Over the past 30 years, MMPs have been considered to be attractive cancer targets, and several different types of synthetic inhibitors have been identified as anticancer agents, but only a small number of small MMPIs have been examined in clinical trials, and none of these molecules has been established as anticancer drugs due to their adverse effects. One major possibility is that the MMPIs used in clinical trials were broad-spectrum drugs that also inhibited the anti-tumor effects and influenced the mediation of the normal physiological processes of MMPs. MMP-2 has recently been characterized as the most validated target for cancer. Therefore, the design and synthesis of selective MMP-2 inhibitors would be helpful for the treatment of cancer.