Tahar Lakhlifi

Bio: Tahar Lakhlifi is an academic researcher. The author has contributed to research in topics: Quantitative structure–activity relationship & Chemistry. The author has an hindex of 12, co-authored 116 publications receiving 833 citations.

Moroccan Medicinal plants as inhibitors against SARS-CoV-2 main protease: Computational investigations.

Abstract: The new Corona-virus, recently called the severe acute respiratory syndrome Coronavirus (SARS-CoV-2) appears for the first time in China and more precisely in Wuhan (December 2019). This disease ca...

Identification of a novel dual-target scaffold for 3CLpro and RdRp proteins of SARS-CoV-2 using 3D-similarity search, molecular docking, molecular dynamics and ADMET evaluation.

Abstract: The new SARS-CoV-2 coronavirus is the causative agent of the COVID-19 pandemic outbreak that affected whole the world with more than 6 million confirmed cases and over 370,000 deaths At present, there are no effective treatments or vaccine for this disease, which constitutes a serious global health crisis As the pandemic still spreading around the globe, it is of interest to use computational methods to identify potential inhibitors for the virus The crystallographic structures of 3CLpro (PDB: 6LU7) and RdRp (PDB 6ML7) were used in virtual screening of 50000 chemical compounds obtained from the CAS Antiviral COVID19 database using 3D-similarity search and standard molecular docking followed by ranking and selection of compounds based on their binding affinity, computational techniques for the sake of details on the binding interactions, absorption, distribution, metabolism, excretion, and toxicity prediction; we report three 4-(morpholin-4-yl)-1,3,5-triazin-2-amine derivatives; two compounds (2001083-68-5 and 2001083-69-6) with optimal binding features to the active site of the main protease and one compound (833463-19-7) with optimal binding features to the active site of the polymerase for further consideration to fight COVID-19 The structural stability and dynamics of lead compounds at the active site of 3CLpro and RdRp were examined using molecular dynamics (MD) simulation Essential dynamics demonstrated that the three complexes remain stable during simulation of 20 ns, which may be suitable candidates for further experimental analysis As the identified leads share the same scaffold, they may serve as promising leads in the development of dual 3CLpro and RdRp inhibitors against SARS-CoV-2Communicated by Ramaswamy H Sarma

Essentials Of Computational Chemistry Theories And Models

Abstract: The fact that a new text book introducing the essentials of computational chemistry contains more than 500 pages shows impressively the grown and still growing size and importance of this field of chemistry. The author’s objectives of the book, using his own words, are “to provide a survey of computational chemistry its underpinnings, its jargon, its strengths and weaknesses that will be accessible to both the experimental and theoretical communities”. This design as a general introduction into computational chemistry makes it an alternative to Andrew R. Leach’s well-established “Molecular Modeling” (Prentice Hall) and Frank Jensen’s “Introduction to Computational Chemistry” (Wiley), although the latter focuses on the theory of electronic structure methods. Cramer’s “Essentials” covers force field and molecular orbital theory, Monte Carlo and Molecular Dynamics simulations, thermodynamic and electronic (spectroscopic) property calculation, condensed phase treatment and a few more topics. Moreover, the book contains thirteen selected case studies sexamples taken from the literature sto illustrate the application of the just presented theoretical and computational models. This especially makes the text book well suited for both classroom discussion and self-study. Each chapter of “Essentials” covers a main topic of computational chemistry and will be briefly described here; all chapters are ended by a bibliography and suggested additional readings as well as the literature references cited in the text. In chapter 1 the author defines basic terms such as “theory”, “model”, and “computation”, introduces the concept of the potential energy surface and provides some general considerations about hardware and software. Interestingly, the first equation occurring in the text is not Schro ̈dinger’s equation, as is the case for most computational chemistry introductions, but the famous Einstein relation. The second chapter deals with molecular mechanics. It explains the different potential energy contributions, introduces the field of structure optimization, and provides an overview of the variety of modern force fields. Chapter 3 covers the simulation of molecular ensembles. It defines phase space and trajectories and shows the formalism of, and problems and difference between, Monte Carlo and molecular dynamics. In chapter 4 the author introduces the foundations of molecular orbital theory. Basic concepts such as Hamilton operator, LCAO basis set approach, many-electron wave functions, etc. are explained. To illuminate the LCAO variational process, the Hu ̈ckel theory is presented with an example. Chapter 5 deals with semiempirical molecular orbital (MO) theory. Besides the classical approaches (extended Hu ̈ckel, CNDO, INDO, NDDO) and methods (e.g., MNDO, AM1, PM3) and their performance, examples are provided from the ongoing development in that still fascinating area. Ab initio MO theory is presented in chapter 6; the basis set concept is discussed in detail, and, after some considerations from an user’s point of view, the general performance of ab initio methods is explicated. The next chapter covers the problem of electron correlation and gives the most prominent solutions for its treatment: configuration interaction, theory of the multiconfiguration self-consistent field, perturbation, and coupled cluster. Practical issues are also discussed. Chapter 8’s topic is density functional theory (DFT). Its theoretical foundation, methodology, and some functionals as well as its pros and cons compared to MO theory are presented together with a general performance overview. The next two chapters deal with charge distribution, derived and spectroscopic properties (e.g., atomic charges, polarizability, rotational, vibrational, and NMR spectra), and thermodynamic properties (e.g., zero-point vibrational energy, free energy of formation, and reaction). The modeling of condensed phases is addressed in chapters 11 (implicit models) and 12 (explicit models), which closes with a comparison between the two approaches. Chapter 13 familiarizes the reader with hybrid quantum mechanical/molecular mechanical (QM/MM) models. Polarization as well as the problematic implications of unsaturated QM and MM components are discussed, and empirical valence bond methods are also presented. The treatment of excited states is the topic of chapter 14; besides CI and MCSCF as computational methods, transition probabilities and solvatochromism are discussed. The last chapter deals with reaction dynamics, mostly adiabaticskinetics, rate constants, reaction paths, and transition state theory are section topics here sbut also nonadiabatic, introducing curve crossing and Marcus theory in brief. The appendix is divided into four parts: an acronym glossary (which is very helpful), an overview of symmetry and group theory, an introduction to spin algebra, and finally a section about orbital localization. A rather detailed index ends the book. The “Essentials” writing style fits the fascinating topic: one reads on and on andssurprise! sanother chapter has been absorbed. The text is complemented by a large number of black and white figures and clear tables, mostly self-explanatory with descriptive captions. The use of equations and mathematical formulas in general is well-balanced, and the level of math should be understandable for every natural scientist with some basic knowledge of physics. There are only a few minor shortcomings: for example, a literature reference cited in the text (“Beck et al.”, p 142) is missing in the bibliography; “Kronecker” is mistyped with o ̈; and the author completely forgot to reference Leach’s text book when referring to other computational chemistry introductions. However, the author has established a specific errata web page (http://pollux.chem.umn.edu/ ∼cramer/Errors.html) with all known errors. These will be corrected in the next printing or next revised edition, respectively. With its emphasis, on one hand, on the basic concepts and applications rather than pure theory and mathematics, and on the other hand, coverage of quantum mechanical and classical mechanical models including examples from inorganic, organic, and biological chemistry, “Essentials” is a useful tool not only for teaching and learning but also as a quick reference, and thus will most probably become one of the standard text books for computational chemistry.

An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study.

Abstract: A new strain of a novel infectious disease affecting millions of people, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently been declared as a pandemic by the World...