Anticancer Drug Discovery

 Computational drug design has successfully facilitated the discovery of several new anticancer drugs that have marked milestones in this field. Molecular modeling, molecular docking, and quantum mechanics have proven to be crucial in modern drug discovery. Since computational methods can cover almost every step of the drug discovery process, applying computational methods to cancer drug discovery has great advantages in terms of investment, resources, and time required. More recently, computational methods such as molecular docking and molecular modeling have been successful in the development of modern anticancer drugs such as Erlotinib, Sorafenib, Lapatinib, Abiraterone, and Crizotinib. We have been using computational methods for the development of small molecule drugs that can be applied to treat cancer or are being processed for the initial stages of clinical trials.

Molecular modeling in drug discovery:

Molecular modeling is one of the techniques that is proving to be a game-changer in addressing the obstacles faced by drug discovery research. Although molecular modeling is a broad field, molecular docking, MD simulation, and ADMET modeling represent the three most widely used components of computational modeling and have been crucial in the identification of lead compounds for experimental in vitro and in vivo testing.

Currently, we are using these techniques for the i) design of small fluorescent biomolecules as the probes for the detection of biomarkers, ii) design and discovery of anticancer lead compounds, and iii) drug-repurposing. 

Fluorescent probes for bio-analyte detection:

 The development of small molecules as fluorescent probes has become increasingly important for the detection and imaging of bio-analytes such as biomarker proteins, cysteine, metal cations, and various anions.  The small molecular fluorescent probes are simple, show high selectivity, and sensitivity, whilst being non-invasive, and are suitable for real-time analysis of living systems. With this perspective, we work on the sensing mechanisms including Förster resonance energy transfer (FRET), intramolecular charge transfer (ICT), photoinduced electron transfer (PeT), excited-state intramolecular proton transfer (ESIPT), aggregation-induced emission (AIE) and multiple modality fluorescence approaches including dual/triple sensing mechanisms (DSM or TSM). We strive to find solutions to the various challenges in the development of small-molecule fluorescent probes suitable for biosensing and live-cell imaging applications.

Supramolecular architectures for molecular recognition:

Mimicry of the molecular recognition features of naturally occurring proteins by synthetic receptors is one of the challenging research topics of supramolecular chemistry. Biological receptors consist of large linear molecules that form 3D structures by specific intermolecular interactions. The recognition site offers precise stereochemistry and exhibits very efficient recognition processes by means of specific functional groups that constitute the entrance and inner surface of the cavity. The presence of specific functional groups at the mouth of the cavity suggests their role in the accessibility of substrates into the cavity. 

The pH of a solution shows a significant effect on the dynamics of the gate (formed by eight benzylic functions) and the portal on the hydrophobic cavity of the receptor. At pH 5.8 the gate closes and prohibits the entry of anionic guests. However, at pH 7.3 the gate opens and allows the entry of anionic guests into the hydrophobic cavity. It is the first time that an anionic receptor efficiently recognizes anionic guests.

 Biomarker detection:

Development of an abiotic fluorescent probe for the detection of cancer-specific antigens. Detection of cancer biomarkers in serum is the hallmark of the development of molecular diagnostics. Detecting blood-based cancer-specific biomarkers allow identifying cancer patients from the general population. The cancer biomarker such as CEA serum has low (2.5 - 3.0 ng mL−1) levels in healthy individuals than in patients (> 3.0 ng mL−1) with several types of cancers, including colorectal carcinoma, colon adenocarcinoma, lung cancer, breast cancer, and gastric cancer. Various methods exist to detect CEA, including ELISAs, colorimetric assays, fluorescence assays, surface-enhanced Raman scattering (SERS), and DNA chips. The common disadvantages of these methods include requisite incubation time, the requirement of highly trained professionals, and expensive instrumentation. On the contrary, the fluorescence method is advantageous because it is ultra-fast, easy to operate, real-time, and low-cost. Therefore, an abiotic, highly-specific fluorescent probe would obviate the current immunoassay-based methods in favor of an abiotic, highly-specific fluorescent probe. Bioinformatics techniques, including molecular modeling and molecular docking, have a high potential in designing and developing small fluorescent molecular probes to detect blood-based cancer biomarkers.

 Biotechnology / Nanomaterial’s as therapeutics:

The functionalized calixarene derivatives exhibit remarkable properties towards organic and bioorganic molecules. However, the ability of calixarene derivatives to form stable complexes with biomolecules allows them to be applied to the development of biosensors in the field of biology, biotechnology, and drug discovery.