New Co(II), Ni(II) and Cu(II) complexes were prepared from thiophene derivative and then characterized to elucidate their chemical formulae. IR-spectral data suggested a monobasic tridentate binding mode for the ligand towards the metal ions within mono-nuclear complexes. Ligand filed transitions as well as magnetic susceptibility, orient strongly for square-planer geometry with Ni(II) and Cu(II) complexes, while octahedral geometry for Co(II) complex. Mass spectroscopy and TGA were performed for complexes to assess on their molecular formulae and the molecular ion peak is attributing to dehydrating complex (M+-nH2O). TEM, EDX and XRD were carried out to indicate morphology, crystallinity and chemical composition of tested complexes. The crystal data estimated, reflect nanometer sizes of studied complexes. DFT method was utilized to obtain optimized structures under 6-31G and LANL2DZ basis sets. Hirshfeld surface properties were estimated for 3D crystal models of complexes, to put view about the contact strength within crystal packing. 2D-fingerprint plots for elemental contribution, clarify the effective contribution of O and H atoms in surface contact between crystals. Cu (II) complex showed greatest potent cytotoxic profile against MCF-7, HepG2 and PC-3 carcinoma cell lines, by IC50s 2.2, 2.6 and 2.1 μg, respectively. High killing rate for tumor cells was observed with an early apoptotic pathway under treatment with all compounds. Also, Cu(II) complex stimulates necrosis killing effect on prostate (PC-3) and breast (MCF-7) cancer cells. Ligand-based pharmacophore methodology, was performed to indicate the most suitable contact sites in compounds towards 1z8l & 3rcd proteins. The search hits several compounds reach 3,732,214 hits and a closer 3D-fingerprint drug model was obtained. MOE docking was performed for most compounds to explain all interaction features through such simulation process. Best docking scores were recorded with HL-3rcd, Co(II)complex-1z8l, Co(II) complex-3rcd and Cu(II) complex-3rcd by values of −60,628, −6.1447, −6.055 and −6.0626, respectively. Amino acid residues that contributing in allosteric binding were clearly categorized. Finally in-silico approach confirms the superiority of Co(II)-L, Cu(II)-L and free thiophene derivative in controlling human cancer cells, which agree with in vitro results. Apoptosis of tested ligand and its complexes against three selected tumor cell-lines. Display omitted •Synthesis for new nonmetric thiophene complexes, analytical and spectral characterization techniques were implemented.•Crustal surface properties as well as molecular modeling features were estimated.•Antitumor activity screening as well as the apoptosis behavior towards three human cancer cells, were investigated.•In-silico approaches were utilized to confirm and simulate antitumor efficiency.