Current Chemical Biology - Volume 12, Issue 1, 2018

Background: Now-a-days, drug design is an important area of research in medicinal chemistry and theoretical aspects of it basically involve molecular docking. Therefore, a detailed knowledge of drug targets, de facto of proteins/enzymes, is essential and thus it has created interest in the study of protein structure and its flexible nature. Objective: The article aims to describe in detail the flexible nature of proteins and its implication in drug design. Method: A detailed survey of the studies on protein flexibility has been made and critically reviewed. Results: Proteins have been found to possess conformational flexibility. They possess an ensemble of conformations. Now the theory of protein-ligand binding has greatly shifted from lock-and-key model to induced-fit model. Since the current concept assumes that protein can exist in many conformations, a ligand can bind to any conformation depending upon its shape and size and thus ligand of any size can be considered to interact with the protein. Conclusion: Protein flexibility stands out to be one of the most important and challenging issues for binding and discovering the potent drugs. Proteins may possess several conformations, but to study the nature of the binding site in them, one must consider its binding partner. Thus, only that conformation of protein is involved in the binding in which the structure of binding site is complementary to that of ligand.

Background: Protein-protein interactions embody the main target of drug discovery due to their vast presence in physiological mechanisms. Hence, targeting protein-protein interfaces is actually the “holy grail” of pharmacology. Much is known about the binding of small molecules to single peptide chains, but much more is still to be discovered about macromolecular complexes and how binding can be affected by modulators. In this scenario, the link between relative flexibility and druggability of protein targets has two very distinctive faces depending upon the orthosteric/allosteric paradigm of drug action. In the orthosteric paradigm, the ‘hot spots’ for ligand binding are those residues endowed with higher flexibility. Conclusion: This stems from the large amount of observations pointing to natively unfolded tracts of protein sequences as responsible for protein-protein interactions. Given the interaction with other macromolecules is the core of protein physiological role, in a local (orthosteric) paradigm of pharmacological action, we maximize the probability of perturbing the system by an agent binding in the same place where such interaction takes place: the most flexible parts of the structure. In the case of an allosteric (non-local) paradigm, the focus shifts toward the signal transmission across the protein molecule: this renders the ‘most promising’ binding sites those residues with the most ‘central’ position that have the higher probability, when perturbed by a ligand, to generalize the perturbation to the entire structure. Protein contact network (PCN) formalism allows for a rational, structure based approach to both the drug action modes.

Background: The functions of all proteins in the biological world are attributed to their flexibility. The highly dynamical nature of proteins allows the binding of various endogenous ligands and substrates that are essential to carry out normal functions in all organisms. Since proteins play an indispensable role in the chemistry that sustains life, it is imperative to understand their functions and more importantly their dynamic behavior and harness this knowledge to design effective chemical agents as therapeutic aids. Objective: The purpose of this review is to discuss the importance of considering flexibility in molecular modeling tools, particularly molecular docking and Quantitative Structure-Activity Relationship (QSAR), to accurately predict the binding conformation of drugs to their protein targets. More emphasis is laid on understanding the importance of modeling protein flexibility of crucial HIV-1 protein targets that has led to the design of potent anti-HIV drugs by molecular docking and QSAR. Conclusion: We have emphasized the importance of incorporating receptor flexibility in molecular docking and QSAR studies. The benefits of allowing receptor flexibility during docking small molecules are vividly evident as the rate of picking false positives is significantly reduced. Similarly, the mechanism of binding and the type of interactions that dominate to exhibit tight binding can be explained by higher dimensional QSAR models, i.e., 4D-QSAR, which includes conformational flexibility.

Background: The novel drug discovery of HIV- 1 integrase inhibitors is based on exploring protein flexibility and QSAR studies using the protein structure. In this pursuit, several novel inhibitors are under development. For example, Allosteric inhibitors (ALLINIs) and Multimerization integrase inhibitors (MINIs). Objective: The objective is to discuss the development process of drug discovery and review the latest developments in HIV-1 integrase inhibitors. Method: A search of scientific literature and data on recent developments of HIV-1 integrase with an intension of safe and effective drugs which inhibits the HIV-1 integrase. The information was organized with an objective of giving Compressive developments leading to the discovery of integrase inhibitors based on protein flexibility, simulation studies and QSAR. Results: Identification of structural details and understanding the binding sites as lead to develop new chemical entities which are promising integrase inhibitors. The role of protein flexibility in developing novel inhibitors like ALLINIs and MINIs. For example Cabotegravir, Elvitegravir, Raltegravir and Dolutegravir. Conclusion: Due to nonavailability of HIV-1 integrase in the crystalline form, we have to use the approach of analogue crystal, for example, PFV integrase. Although there are a drastic difference in the structural features in HIV-1 and PFV integrase. Researchers have to depend on PFV integrase for developing HIV-1 integrase inhibitors by trial and error process.

Hsp90 is a molecular chaperone which is engaged in the repair of diverse oncogenic proteins. Additionally, it is overexpressed in cancer cells along with co-chaperones, whereas normal cell Hsp90 (less than 2 % of cellular proteins) resides in an uncomplexed state. Hence, this chaperone is an encouraging target for the discovery of novel chemical entities against cancer. Proteins execute their functions by interacting with various macromolecules. The conformational flexibility of polypeptides helps them to adopt a shape corresponding to their partner molecules. Hsp90 is a highly flexible polypeptide which can accommodate a wide variety of dynamic states. The major cause for this structural dynamism is the intrinsic flexibility of the protein. In this review, the structure and function of Hsp90 chaperone are discussed. This is followed by a description of the factors regulating the proteins flexibility. Finally, dynamics dependent drug designing strategy (induce fit docking and molecular dynamics simulation) for the discovery of novel Hsp90 inhibitors is discussed.

Background: NS5B polymerase remains an important anti-hepatitis C virus (HCV) drug target. It has been well reported that ligand binding induces large conformational changes in the receptor. Several computational models describing polymerase dynamics have been reported. Various conformational forms have been determined by crystallography and NMR experiments and they suggest the binding of HCV inhibitors in allosteric sites might affect polymerase flexibility. Objective: In most of the cases of structure-based drug design (SBDD), only static structures have been given consideration and most molecular modeling studies have recognized the importance of flexibility. The standard virtual docking methods using rigid receptor may give misleading results as in reality many proteins undergo side-chain and/or backbone movements. The importance of HCV NS5B polymerase receptor flexibility in altering the binding site to complement the shape and binding mode of the ligand i.e. induced fit docking need to be considered. Method: The various methodologies were adopted for molecular modeling based on induced-fit docking at the well-defined inhibitor binding sites i.e. “palm” and “thumb” domain. Some of the well reported NNIs and NIs are VX-222, ANA598/Setrobuvir, CS01, aureusidin, N,N-disubstituted phenylalanine, benzothiadiazine, 6-aminoquinoline derivatives, etc. Results: These assumptions have lead to application of quantum mechanics and induced-fit docking for the development of various HCV NS5B polymerase inhibitors. This enzyme has proved to be challenging and therefore potential ligands with structural diversity have been modified to enhance selectivity and affinity. The flexible nature of HCV polymerase, reveals details about substrate-inhibitor interaction to its active site within the membrane. Conclusion: It will help to develop allosteric inhibitors into efficient drugs by understanding their indirect mode of action and complex structure-activity/kinetic relationship.

Background: Interest in targeting metabolism as a viable cancer therapy has been revived in last decade. This has significantly contributed to the understanding of the altered metabolic profile of proliferating cancer cells. Clinically launched target specific drugs have shown encouraging results in terms of both efficacy and safety than conventional anticancer drugs. Objective: Targeted approaches have significantly changed the treatment of cancer and substantially improved life expectancy of cancer patients. Moreover, the continual discovery of novel molecular targets against various cancer subtypes (lung, breast, colon, prostate, pancreatic cancer etc.) has enabled early diagnosis and treatment of patients against this dreadful disease. Identification of novel cancer biomarkers may aid in the development of new anti-cancer therapies and treatment strategies. Conclusion: Molecular mechanism and clinical efficacy of some of the emerging molecular targets for cancer chemotherapy have been briefly reviewed in the present article.

Background: Protein S (PS) is a natural anticoagulant that has a vital function in regulating hemostasis and inflammation. Recently, the physiological and functional aspects of PS have gained considerable attention, whereas the biophysical properties of PS are far less well defined. Objective: In this study, our goal was to improve the yield of recombinant PS with minimal contamination by endogenous, host cell PS. Method: PS-stable cell lines were exposed to external factors and analyzed by qPCR and immunoblotting for endogenous and exogenous PS levels. Results: Glucose treatment decreased the overall yield of endogenous and exogenous PS, hydrogen peroxide treatment increased the yield of both endogenous and exogenous PS, and calcium chloride treatment increased secretion of exogenous PS without affecting secretion of endogenous PS. Conclusion: Supplementation of the expression medium with 5 mM calcium chloride improves the yield of recombinant PS.